2-240744058-G-A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6BP7BS1

The NM_001244008.2(KIF1A):c.3468C>T(p.Ile1156Ile) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000648 in 1,604,400 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. I1156I) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.00032 ( 0 hom., cov: 33)

Exomes 𝑓: 0.000039 ( 0 hom. )

Consequence

KIF1A
NM_001244008.2 splice_region, synonymous

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:3

Conservation

PhyloP100: -0.599

Publications

1 publications found

Variant links:

Genes affected

KIF1A (HGNC:888): (kinesin family member 1A) The protein encoded by this gene is a member of the kinesin family and functions as an anterograde motor protein that transports membranous organelles along axonal microtubules. Mutations at this locus have been associated with spastic paraplegia-30 and hereditary sensory neuropathy IIC. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Apr 2012]

KIF1A Gene-Disease associations (from GenCC):

intellectual disability, autosomal dominant 9
Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
syndromic intellectual disability
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
neuropathy, hereditary sensory, type 2C
Inheritance: AR Classification: DEFINITIVE, STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
hereditary spastic paraplegia 30
Inheritance: AR, AD Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet
autosomal dominant non-syndromic intellectual disability
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
PEHO syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
hereditary sensory and autonomic neuropathy type 2
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

KIF1A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

BP6

Variant 2-240744058-G-A is Benign according to our data. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285. Variant chr2-240744058-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 211285.

BP7

Synonymous conserved (PhyloP=-0.599 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.000315 (48/152328) while in subpopulation AFR AF = 0.00106 (44/41570). AF 95% confidence interval is 0.00081. There are 0 homozygotes in GnomAd4. There are 24 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF1A	NM_001244008.2 link	c.3468C>T	p.Ile1156Ile	splice_region_variant, synonymous_variant	Exon 33 of 49	ENST00000498729.9	NP_001230937.1	Q12756-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF1A	ENST00000498729.9 link	c.3468C>T	p.Ile1156Ile	splice_region_variant, synonymous_variant	Exon 33 of 49	5	NM_001244008.2	ENSP00000438388.1		Q12756-3

Frequencies

GnomAD3 genomes

AF:

0.000309

AC:

AN:

152210

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00104

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000262

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000964

AC:

AN:

248846

AF XY:

0.0000741

show subpopulations

Gnomad AFR exome

AF:

0.000969

Gnomad AMR exome

AF:

0.0000870

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000111

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.000497

GnomAD4 exome

AF:

0.0000386

AC:

AN:

1452072

Hom.:

Cov.:

AF XY:

0.0000346

AC XY:

AN XY:

722882

show subpopulations

African (AFR)

AF:

0.000691

AC:

AN:

33296

American (AMR)

AF:

0.000134

AC:

AN:

44690

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26062

East Asian (EAS)

AF:

0.0000505

AC:

AN:

39638

South Asian (SAS)

AF:

0.0000465

AC:

AN:

86018

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53294

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5750

European-Non Finnish (NFE)

AF:

0.0000127

AC:

AN:

1103256

Other (OTH)

AF:

0.000117

AC:

AN:

60068

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000315

AC:

AN:

152328

Hom.:

Cov.:

AF XY:

0.000322

AC XY:

AN XY:

74494

show subpopulations

African (AFR)

AF:

0.00106

AC:

AN:

41570

American (AMR)

AF:

0.000261

AC:

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5184

South Asian (SAS)

AF:

0.00

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10630

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

68026

Other (OTH)

AF:

0.00

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000247

Hom.:

Bravo

AF:

0.000468

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1Benign:3

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not provided

Benign:2

Jan 21, 2019

Athena Diagnostics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jan 15, 2021

GeneDx

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Uncertain:1

Nov 04, 2014

Genetic Services Laboratory, University of Chicago

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Neuropathy, hereditary sensory, type 2C;C5235139:Hereditary spastic paraplegia 30;C5393830:Intellectual disability, autosomal dominant 9

Benign:1

Jan 30, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

5.7

(source)

DANN

Benign

0.83

PhyloP100

-0.60

Mutation Taster

=95/5

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over