dbSNP rs152189: KIF2A:c.2150-863T>C (chr5-62384621-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001098511.3(KIF2A):c.2150-863T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,128 control chromosomes in the GnomAD database, including 4,697 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.25 ( 4697 hom., cov: 32)

Consequence

KIF2A
NM_001098511.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Publications

8 publications found

Variant links:

Genes affected

KIF2A (HGNC:6318): (kinesin family member 2A) The protein encoded by this gene is a plus end-directed motor required for normal mitotic progression. The encoded protein is required for normal spindle activity during mitosis and is necessary for normal brain development. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

KIF2A links:

ENSG00000288643 (HGNC:):

ENSG00000288643 links:

DIMT1 (HGNC:30217): (DIM1 rRNA methyltransferase and ribosome maturation factor) The protein encoded by this gene is a methyltransferase that is responsible for dimethylation of adjacent adenosines near the 18S rRNA decoding site. The encoded protein is essential for ribosome biogenesis, although its catalytic activity is not involved in the process. The yeast ortholog of this protein functions in the cytoplasm while this protein functions in the nucleus. [provided by RefSeq, Jan 2017]

DIMT1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
KIF2A	NM_001098511.3 link	c.2150-863T>C	intron_variant	Intron 20 of 20	ENST00000407818.8	NP_001091981.1
KIF2A	NM_004520.5 link	c.2036-863T>C	intron_variant	Intron 19 of 19		NP_004511.2
KIF2A	NM_001243953.2 link	c.1979-863T>C	intron_variant	Intron 19 of 19		NP_001230882.1
KIF2A	NM_001243952.2 link	c.1955-863T>C	intron_variant	Intron 20 of 20		NP_001230881.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF2A	ENST00000407818.8 link	c.2150-863T>C		intron_variant	Intron 20 of 20	1	NM_001098511.3	ENSP00000385000.3
ENSG00000288643	ENST00000509663.2 link	n.64+78085T>C		intron_variant	Intron 1 of 5	3		ENSP00000502199.1

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37455

AN:

152010

Hom.:

4697

Cov.:

show subpopulations

Gnomad AFR

AF:

0.264

Gnomad AMI

AF:

0.425

Gnomad AMR

AF:

0.203

Gnomad ASJ

AF:

0.284

Gnomad EAS

AF:

0.230

Gnomad SAS

AF:

0.182

Gnomad FIN

AF:

0.230

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.250

Gnomad OTH

AF:

0.219

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.246

AC:

37472

AN:

152128

Hom.:

4697

Cov.:

AF XY:

0.245

AC XY:

18258

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.263

AC:

10931

AN:

41496

American (AMR)

AF:

0.203

AC:

3104

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.284

AC:

986

AN:

3468

East Asian (EAS)

AF:

0.229

AC:

1186

AN:

5176

South Asian (SAS)

AF:

0.182

AC:

876

AN:

4824

European-Finnish (FIN)

AF:

0.230

AC:

2440

AN:

10592

Middle Eastern (MID)

AF:

0.303

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.250

AC:

17011

AN:

67964

Other (OTH)

AF:

0.218

AC:

461

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1454

2907

4361

5814

7268

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

384

768

1152

1536

1920

<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:

0.241

Hom.:

749

Bravo

AF:

0.247

Asia WGS

AF:

0.197

AC:

687

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.54

(source)

DANN

Benign

0.44

PhyloP100

-1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over