Variant chr1-200553223-A-T 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_014875.3(KIF14):c.*165T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 712,532 control chromosomes in the GnomAD database, including 117,908 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.53 ( 22138 hom., cov: 33)

Exomes 𝑓: 0.58 ( 95770 hom. )

Consequence

KIF14
NM_014875.3 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0260

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 1-200553223-A-T is Benign according to our data. Variant chr1-200553223-A-T is described in ClinVar as [Benign]. Clinvar id is 1286174.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 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.*165T>A		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.*165T>A		3_prime_UTR_variant	30/30	2	NM_014875.3	P1
KIF14	ENST00000614960.4 linkuse as main transcript	c.*165T>A		3_prime_UTR_variant	29/29	1		P1

Frequencies

GnomAD3 genomes

AF:

0.530

AC:

80579

AN:

151958

Hom.:

22136

Cov.:

show subpopulations

Gnomad AFR

AF:

0.387

Gnomad AMI

AF:

0.577

Gnomad AMR

AF:

0.555

Gnomad ASJ

AF:

0.653

Gnomad EAS

AF:

0.690

Gnomad SAS

AF:

0.641

Gnomad FIN

AF:

0.523

Gnomad MID

AF:

0.617

Gnomad NFE

AF:

0.583

Gnomad OTH

AF:

0.592

GnomAD4 exome

AF:

0.580

AC:

325264

AN:

560456

Hom.:

95770

Cov.:

AF XY:

0.583

AC XY:

167937

AN XY:

288138

show subpopulations

Gnomad4 AFR exome

AF:

0.385

Gnomad4 AMR exome

AF:

0.512

Gnomad4 ASJ exome

AF:

0.661

Gnomad4 EAS exome

AF:

0.691

Gnomad4 SAS exome

AF:

0.639

Gnomad4 FIN exome

AF:

0.520

Gnomad4 NFE exome

AF:

0.579

Gnomad4 OTH exome

AF:

0.581

GnomAD4 genome

AF:

0.530

AC:

80614

AN:

152076

Hom.:

22138

Cov.:

AF XY:

0.532

AC XY:

39536

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.387

Gnomad4 AMR

AF:

0.555

Gnomad4 ASJ

AF:

0.653

Gnomad4 EAS

AF:

0.690

Gnomad4 SAS

AF:

0.641

Gnomad4 FIN

AF:

0.523

Gnomad4 NFE

AF:

0.583

Gnomad4 OTH

AF:

0.593

Alfa

AF:

0.535

Hom.:

2753

Bravo

AF:

0.524

Asia WGS

AF:

0.659

AC:

2291

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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

-0.90

CADD

Benign

1.8

DANN

Benign

0.75

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