Variant 5-62347942-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001098511.3(KIF2A):c.160-106G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0684 in 1,269,498 control chromosomes in the GnomAD database, including 3,366 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.056 ( 324 hom., cov: 32)

Exomes 𝑓: 0.070 ( 3042 hom. )

Consequence

KIF2A
NM_001098511.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0220

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 5-62347942-G-A is Benign according to our data. Variant chr5-62347942-G-A is described in ClinVar as [Benign]. Clinvar id is 1271265.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
KIF2A	NM_001098511.3 linkuse as main transcript	c.160-106G>A	intron_variant	ENST00000407818.8	NP_001091981.1	O00139-4
KIF2A	NM_004520.5 linkuse as main transcript	c.160-106G>A	intron_variant		NP_004511.2	O00139-3
KIF2A	NM_001243953.2 linkuse as main transcript	c.160-106G>A	intron_variant		NP_001230882.1	A0A6Q8PFA6B0AZS5
KIF2A	NM_001243952.2 linkuse as main transcript	c.79-106G>A	intron_variant		NP_001230881.2	O00139-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF2A	ENST00000407818.8 linkuse as main transcript	c.160-106G>A		intron_variant		1	NM_001098511.3	ENSP00000385000.3		O00139-4
ENSG00000288643	ENST00000509663.2 linkuse as main transcript	n.64+41406G>A		intron_variant		3		ENSP00000502199.1		A0A6Q8PGD0

Frequencies

GnomAD3 genomes

AF:

0.0560

AC:

8515

AN:

151928

Hom.:

323

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0171

Gnomad AMI

AF:

0.0439

Gnomad AMR

AF:

0.0425

Gnomad ASJ

AF:

0.0788

Gnomad EAS

AF:

0.134

Gnomad SAS

AF:

0.0370

Gnomad FIN

AF:

0.100

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0702

Gnomad OTH

AF:

0.0591

GnomAD4 exome

AF:

0.0701

AC:

78373

AN:

1117452

Hom.:

3042

AF XY:

0.0689

AC XY:

38351

AN XY:

556432

show subpopulations

Gnomad4 AFR exome

AF:

0.0143

Gnomad4 AMR exome

AF:

0.0306

Gnomad4 ASJ exome

AF:

0.0758

Gnomad4 EAS exome

AF:

0.118

Gnomad4 SAS exome

AF:

0.0321

Gnomad4 FIN exome

AF:

0.103

Gnomad4 NFE exome

AF:

0.0725

Gnomad4 OTH exome

AF:

0.0676

GnomAD4 genome

AF:

0.0560

AC:

8514

AN:

152046

Hom.:

324

Cov.:

AF XY:

0.0567

AC XY:

4216

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.0172

Gnomad4 AMR

AF:

0.0425

Gnomad4 ASJ

AF:

0.0788

Gnomad4 EAS

AF:

0.135

Gnomad4 SAS

AF:

0.0364

Gnomad4 FIN

AF:

0.100

Gnomad4 NFE

AF:

0.0702

Gnomad4 OTH

AF:

0.0585

Alfa

AF:

0.0636

Hom.:

Bravo

AF:

0.0500

Asia WGS

AF:

0.0780

AC:

271

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 11, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.2

DANN

Benign

0.54

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

LitVar

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over