Variant chr16-29799998-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_007317.3(KIF22):c.1230C>T(p.Ile410=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.984 in 1,613,950 control chromosomes in the GnomAD database, including 783,587 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.92 ( 65445 hom., cov: 32)

Exomes 𝑓: 0.99 ( 718142 hom. )

Consequence

KIF22
NM_007317.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0740

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 16-29799998-C-T is Benign according to our data. Variant chr16-29799998-C-T is described in ClinVar as [Benign]. Clinvar id is 1170585.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-29799998-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.074 with no splicing effect.

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	UniProt
KIF22	NM_007317.3 linkuse as main transcript	c.1230C>T	p.Ile410=	synonymous_variant	8/14	ENST00000160827.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF22	ENST00000160827.9 linkuse as main transcript	c.1230C>T	p.Ile410=	synonymous_variant	8/14	1	NM_007317.3	P2	Q14807-1

Frequencies

GnomAD3 genomes

AF:

0.919

AC:

139890

AN:

152138

Hom.:

65399

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:

0.935

Gnomad SAS

AF:

0.996

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.981

Gnomad NFE

AF:

0.999

Gnomad OTH

AF:

0.947

GnomAD3 exomes

AF:

0.974

AC:

244585

AN:

251146

Hom.:

119724

AF XY:

0.980

AC XY:

133075

AN XY:

135760

show subpopulations

Gnomad AFR exome

AF:

0.723

Gnomad AMR exome

AF:

0.986

Gnomad ASJ exome

AF:

0.988

Gnomad EAS exome

AF:

0.934

Gnomad SAS exome

AF:

0.998

Gnomad FIN exome

AF:

1.00

Gnomad NFE exome

AF:

0.999

Gnomad OTH exome

AF:

0.986

GnomAD4 exome

AF:

0.990

AC:

1447564

AN:

1461694

Hom.:

718142

Cov.:

AF XY:

0.992

AC XY:

721058

AN XY:

727168

show subpopulations

Gnomad4 AFR exome

AF:

0.725

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:

0.919

AC:

139990

AN:

152256

Hom.:

65445

Cov.:

AF XY:

0.921

AC XY:

68561

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.730

Gnomad4 AMR

AF:

0.970

Gnomad4 ASJ

AF:

0.984

Gnomad4 EAS

AF:

0.936

Gnomad4 SAS

AF:

0.997

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

0.999

Gnomad4 OTH

AF:

0.947

Alfa

AF:

0.970

Hom.:

31108

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:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Spondyloepimetaphyseal dysplasia with multiple dislocations

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

2.6

DANN

Benign

0.58

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