Variant 16-29802913-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_007317.3(KIF22):c.1425G>A(p.Val475Val) variant causes a synonymous change. The variant allele was found at a frequency of 0.984 in 1,612,538 control chromosomes in the GnomAD database, including 783,002 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.92 ( 65366 hom., cov: 29)

Exomes 𝑓: 0.99 ( 717636 hom. )

Consequence

KIF22
NM_007317.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 3.71

Variant links:

Genes affected

KIF22 (HGNC:6391): (kinesin family member 22) The protein encoded by this gene is a member of the kinesin-like protein family. The family members are microtubule-dependent molecular motors that transport organelles within cells and move chromosomes during cell division. The C-terminal half of this protein has been shown to bind DNA. Studies with the Xenopus homolog suggests its essential role in metaphase chromosome alignment and maintenance. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

KIF22 links:

KIF22 (HGNC:):

KIF22 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=-0.57).

BP6

Variant 16-29802913-G-A is Benign according to our data. Variant chr16-29802913-G-A is described in ClinVar as [Benign]. Clinvar id is 803248.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-29802913-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF22	NM_007317.3 linkuse as main transcript	c.1425G>A	p.Val475Val	synonymous_variant	9/14	ENST00000160827.9	NP_015556.1	Q14807-1
KIF22	NM_001256269.2 linkuse as main transcript	c.1221G>A	p.Val407Val	synonymous_variant	10/15		NP_001243198.1	Q14807-2A0A024R632
KIF22	NM_001256270.1 linkuse as main transcript	c.1221G>A	p.Val407Val	synonymous_variant	9/14		NP_001243199.1	Q14807-2A0A024R632B7Z9T5
KIF22	XM_047434094.1 linkuse as main transcript	c.1425G>A	p.Val475Val	synonymous_variant	9/11		XP_047290050.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF22	ENST00000160827.9 linkuse as main transcript	c.1425G>A	p.Val475Val	synonymous_variant	9/14	1	NM_007317.3	ENSP00000160827.5		Q14807-1

Frequencies

GnomAD3 genomes

AF:

0.920

AC:

139706

AN:

151920

Hom.:

65321

Cov.:

show subpopulations

Gnomad AFR

AF:

0.730

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.970

Gnomad ASJ

AF:

0.984

Gnomad EAS

AF:

0.934

Gnomad SAS

AF:

0.996

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.981

Gnomad NFE

AF:

0.999

Gnomad OTH

AF:

0.948

GnomAD3 exomes

AF:

0.974

AC:

243375

AN:

249880

Hom.:

119142

AF XY:

0.980

AC XY:

132463

AN XY:

135116

show subpopulations

Gnomad AFR exome

AF:

0.724

Gnomad AMR exome

AF:

0.986

Gnomad ASJ exome

AF:

0.989

Gnomad EAS exome

AF:

0.934

Gnomad SAS exome

AF:

0.999

Gnomad FIN exome

AF:

1.00

Gnomad NFE exome

AF:

0.999

Gnomad OTH exome

AF:

0.986

GnomAD4 exome

AF:

0.990

AC:

1446473

AN:

1460500

Hom.:

717636

Cov.:

AF XY:

0.992

AC XY:

720503

AN XY:

726556

show subpopulations

Gnomad4 AFR exome

AF:

0.726

Gnomad4 AMR exome

AF:

0.985

Gnomad4 ASJ exome

AF:

0.988

Gnomad4 EAS exome

AF:

0.953

Gnomad4 SAS exome

AF:

0.998

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.999

Gnomad4 OTH exome

AF:

0.979

GnomAD4 genome

AF:

0.920

AC:

139805

AN:

152038

Hom.:

65366

Cov.:

AF XY:

0.921

AC XY:

68450

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.730

Gnomad4 AMR

AF:

0.970

Gnomad4 ASJ

AF:

0.984

Gnomad4 EAS

AF:

0.935

Gnomad4 SAS

AF:

0.997

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

0.999

Gnomad4 OTH

AF:

0.948

Alfa

AF:

0.961

Hom.:

30778

Bravo

AF:

0.907

Asia WGS

AF:

0.960

AC:

3339

AN:

3478

EpiCase

AF:

0.998

EpiControl

AF:

0.999

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Spondyloepimetaphyseal dysplasia with multiple dislocations

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Aug 19, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

7.9

DANN

Benign

0.59

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

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