Variant 1-200553141-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_014875.3(KIF14):c.*247C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 237,336 control chromosomes in the GnomAD database, including 30,648 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.51 ( 19626 hom., cov: 30)

Exomes 𝑓: 0.50 ( 11022 hom. )

Consequence

KIF14
NM_014875.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.82

Variant links:

Genes affected

KIF14 (HGNC:19181): (kinesin family member 14) This gene encodes a member of the kinesin-3 superfamily of microtubule motor proteins. These proteins are involved in numerous processes including vesicle transport, chromosome segregation, mitotic spindle formation, and cytokinesis. In human HeLa-S3 and 293T cells, this protein is localized to the cytoplasm during interphase, to the spindle poles and spindle microtubules during mitosis, and to the midbody during cytokinesis. An internal motor domain displays microtubule-dependent ATPase activity, consistent with its function as a microtubule motor protein. Knockdown of this gene results in failed cytokinesis with endoreplication, which results in multinucleated cells. This gene has been identified as a likely oncogene in breast, lung and ovarian cancers, as well as retinoblastomas and gliomas. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2015]

KIF14 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.03).

BP6

Variant 1-200553141-G-A is Benign according to our data. Variant chr1-200553141-G-A is described in ClinVar as [Benign]. Clinvar id is 1283604.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF14	NM_014875.3 linkuse as main transcript	c.*247C>T		3_prime_UTR_variant	30/30	ENST00000367350.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF14	ENST00000367350.5 linkuse as main transcript	c.*247C>T		3_prime_UTR_variant	30/30	2	NM_014875.3	P1
KIF14	ENST00000614960.4 linkuse as main transcript	c.*247C>T		3_prime_UTR_variant	29/29	1		P1

Frequencies

GnomAD3 genomes

AF:

0.507

AC:

76772

AN:

151560

Hom.:

19632

Cov.:

show subpopulations

Gnomad AFR

AF:

0.489

Gnomad AMI

AF:

0.563

Gnomad AMR

AF:

0.518

Gnomad ASJ

AF:

0.614

Gnomad EAS

AF:

0.627

Gnomad SAS

AF:

0.612

Gnomad FIN

AF:

0.435

Gnomad MID

AF:

0.618

Gnomad NFE

AF:

0.501

Gnomad OTH

AF:

0.540

GnomAD4 exome

AF:

0.500

AC:

42847

AN:

85660

Hom.:

11022

Cov.:

AF XY:

0.504

AC XY:

22389

AN XY:

44444

show subpopulations

Gnomad4 AFR exome

AF:

0.477

Gnomad4 AMR exome

AF:

0.494

Gnomad4 ASJ exome

AF:

0.582

Gnomad4 EAS exome

AF:

0.627

Gnomad4 SAS exome

AF:

0.598

Gnomad4 FIN exome

AF:

0.406

Gnomad4 NFE exome

AF:

0.485

Gnomad4 OTH exome

AF:

0.498

GnomAD4 genome

AF:

0.506

AC:

76804

AN:

151676

Hom.:

19626

Cov.:

AF XY:

0.506

AC XY:

37521

AN XY:

74084

show subpopulations

Gnomad4 AFR

AF:

0.489

Gnomad4 AMR

AF:

0.518

Gnomad4 ASJ

AF:

0.614

Gnomad4 EAS

AF:

0.626

Gnomad4 SAS

AF:

0.611

Gnomad4 FIN

AF:

0.435

Gnomad4 NFE

AF:

0.501

Gnomad4 OTH

AF:

0.539

Alfa

AF:

0.468

Hom.:

2036

Bravo

AF:

0.510

Asia WGS

AF:

0.576

AC:

2001

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.047

DANN

Benign

0.62

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