2-240747320-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2

The NM_001244008.2(KIF1A):​c.2979C>T​(p.Ala993=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00284 in 1,612,432 control chromosomes in the GnomAD database, including 67 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.013 ( 31 hom., cov: 33)
Exomes 𝑓: 0.0018 ( 36 hom. )

Consequence

KIF1A
NM_001244008.2 splice_region, synonymous

Scores

2
Splicing: ADA: 0.000007369
2

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:9

Conservation

PhyloP100: -1.37
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 2-240747320-G-A is Benign according to our data. Variant chr2-240747320-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 129388.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1, Benign=7}. Variant chr2-240747320-G-A is described in Lovd as [Benign]. Variant chr2-240747320-G-A is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=-1.37 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0132 (2007/152256) while in subpopulation AFR AF= 0.0449 (1863/41522). AF 95% confidence interval is 0.0432. There are 31 homozygotes in gnomad4. There are 910 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 31 AD,AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KIF1ANM_001244008.2 linkuse as main transcriptc.2979C>T p.Ala993= splice_region_variant, synonymous_variant 29/49 ENST00000498729.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KIF1AENST00000498729.9 linkuse as main transcriptc.2979C>T p.Ala993= splice_region_variant, synonymous_variant 29/495 NM_001244008.2 Q12756-3

Frequencies

GnomAD3 genomes
AF:
0.0131
AC:
2000
AN:
152138
Hom.:
30
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0448
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00347
Gnomad ASJ
AF:
0.0167
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000191
Gnomad OTH
AF:
0.00860
GnomAD3 exomes
AF:
0.00383
AC:
947
AN:
247502
Hom.:
15
AF XY:
0.00289
AC XY:
389
AN XY:
134618
show subpopulations
Gnomad AFR exome
AF:
0.0446
Gnomad AMR exome
AF:
0.00169
Gnomad ASJ exome
AF:
0.0172
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000206
Gnomad OTH exome
AF:
0.00200
GnomAD4 exome
AF:
0.00176
AC:
2566
AN:
1460176
Hom.:
36
Cov.:
30
AF XY:
0.00152
AC XY:
1106
AN XY:
726408
show subpopulations
Gnomad4 AFR exome
AF:
0.0468
Gnomad4 AMR exome
AF:
0.00195
Gnomad4 ASJ exome
AF:
0.0187
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000464
Gnomad4 FIN exome
AF:
0.0000188
Gnomad4 NFE exome
AF:
0.000121
Gnomad4 OTH exome
AF:
0.00451
GnomAD4 genome
AF:
0.0132
AC:
2007
AN:
152256
Hom.:
31
Cov.:
33
AF XY:
0.0122
AC XY:
910
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.0449
Gnomad4 AMR
AF:
0.00346
Gnomad4 ASJ
AF:
0.0167
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000191
Gnomad4 OTH
AF:
0.00851
Alfa
AF:
0.00364
Hom.:
9
Bravo
AF:
0.0146
Asia WGS
AF:
0.00202
AC:
8
AN:
3478
EpiCase
AF:
0.000491
EpiControl
AF:
0.000416

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:9
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Benign:3
Benign, criteria provided, single submitterclinical testingARUP Laboratories, Molecular Genetics and Genomics, ARUP LaboratoriesMar 04, 2021- -
Benign, criteria provided, single submitterclinical testingAthena DiagnosticsDec 28, 2017- -
Benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenSep 01, 2023KIF1A: BP4, BP7, BS1, BS2 -
Hereditary spastic paraplegia 30 Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitterresearchCenter for Precision Medicine, Vanderbilt University Medical CenterMar 16, 2018- -
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not specified Benign:2
Likely benign, no assertion criteria providedclinical testingGenetic Services Laboratory, University of Chicago-Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
Benign, criteria provided, single submitterclinical testingGeneDxApr 24, 2015This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitterclinical testingAmbry GeneticsMay 11, 2016This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Hereditary spastic paraplegia Benign:1
Likely benign, criteria provided, single submitterclinical testingGenome Diagnostics Laboratory, The Hospital for Sick ChildrenJun 13, 2021- -
Neuropathy, hereditary sensory, type 2C;C5235139:Hereditary spastic paraplegia 30;C5393830:Intellectual disability, autosomal dominant 9 Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeFeb 01, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
CADD
Benign
0.76
DANN
Benign
0.51

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.0000074
dbscSNV1_RF
Benign
0.0
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs116297894; hg19: chr2-241686737; API