Variant rs17085310 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002253.4(KDR):c.1987+28C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0112 in 1,580,432 control chromosomes in the GnomAD database, including 709 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.014 ( 73 hom., cov: 32)

Exomes 𝑓: 0.011 ( 636 hom. )

Consequence

KDR
NM_002253.4 intron

Scores

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: -0.658

Variant links:

Genes affected

KDR (HGNC:6307): (kinase insert domain receptor) Vascular endothelial growth factor (VEGF) is a major growth factor for endothelial cells. This gene encodes one of the two receptors of the VEGF. This receptor, known as kinase insert domain receptor, is a type III receptor tyrosine kinase. It functions as the main mediator of VEGF-induced endothelial proliferation, survival, migration, tubular morphogenesis and sprouting. The signalling and trafficking of this receptor are regulated by multiple factors, including Rab GTPase, P2Y purine nucleotide receptor, integrin alphaVbeta3, T-cell protein tyrosine phosphatase, etc.. Mutations of this gene are implicated in infantile capillary hemangiomas. [provided by RefSeq, May 2009]

KDR links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KDR	NM_002253.4 link	c.1987+28C>T		intron_variant		ENST00000263923.5	NP_002244.1	P35968-1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
KDR	ENST00000263923.5 link	c.1987+28C>T	intron_variant		1	NM_002253.4	ENSP00000263923.4	P35968-1
KDR	ENST00000512566.1 link	n.2015C>T	non_coding_transcript_exon_variant	13/13	1
KDR	ENST00000647068.1 link	n.2000+28C>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.0136

AC:

2072

AN:

152128

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00179

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0574

Gnomad ASJ

AF:

0.00288

Gnomad EAS

AF:

0.0853

Gnomad SAS

AF:

0.0457

Gnomad FIN

AF:

0.0197

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00318

Gnomad OTH

AF:

0.0115

GnomAD3 exomes

AF:

0.0303

AC:

7393

AN:

244128

Hom.:

366

AF XY:

0.0262

AC XY:

3458

AN XY:

132090

show subpopulations

Gnomad AFR exome

AF:

0.00175

Gnomad AMR exome

AF:

0.115

Gnomad ASJ exome

AF:

0.00181

Gnomad EAS exome

AF:

0.0870

Gnomad SAS exome

AF:

0.0317

Gnomad FIN exome

AF:

0.0184

Gnomad NFE exome

AF:

0.00396

Gnomad OTH exome

AF:

0.0186

GnomAD4 exome

AF:

0.0110

AC:

15678

AN:

1428186

Hom.:

636

Cov.:

AF XY:

0.0109

AC XY:

7780

AN XY:

712138

show subpopulations

Gnomad4 AFR exome

AF:

0.00113

Gnomad4 AMR exome

AF:

0.108

Gnomad4 ASJ exome

AF:

0.00190

Gnomad4 EAS exome

AF:

0.0956

Gnomad4 SAS exome

AF:

0.0308

Gnomad4 FIN exome

AF:

0.0197

Gnomad4 NFE exome

AF:

0.00235

Gnomad4 OTH exome

AF:

0.0140

GnomAD4 genome

AF:

0.0136

AC:

2069

AN:

152246

Hom.:

Cov.:

AF XY:

0.0154

AC XY:

1149

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.00178

Gnomad4 AMR

AF:

0.0572

Gnomad4 ASJ

AF:

0.00288

Gnomad4 EAS

AF:

0.0855

Gnomad4 SAS

AF:

0.0452

Gnomad4 FIN

AF:

0.0197

Gnomad4 NFE

AF:

0.00318

Gnomad4 OTH

AF:

0.0118

Alfa

AF:

0.0143

Hom.:

Bravo

AF:

0.0175

Asia WGS

AF:

0.0700

AC:

242

AN:

3478

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

LINK: link

Submissions by phenotype

not specified

Other:1

not provided, no classification provided

reference population

ITMI

Sep 19, 2013

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.23

DANN

Benign

0.41

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