rs2010963

Variant summary

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

The NM_003376(VEGFA):c.-94C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 151946 control chromosomes in the gnomAD Genomes database, including 35315 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.68 ( 35315 hom., cov: 33)

Consequence

VEGFA
NM_003376 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1O:1

Conservation

PhyloP100: 1.03

Links

VEGFA (HGNC:12680):

(HGNC:):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 6:43770613-C>G is Benign according to our data. Variant chr6-43770613-C-G is described in ClinVar as [Benign]. Clinvar id is 12223. Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VEGFA	NM_003376.6 linkuse as main transcript	c.-94C>G		5_prime_UTR_variant	1/8	ENST00000672860.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VEGFA	ENST00000672860.3 linkuse as main transcript	c.-94C>G		5_prime_UTR_variant	1/8		NM_003376.6		P15692-13
	ENST00000607600.1 linkuse as main transcript	n.4G>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.682

AC:

103572

AN:

151946

Hom.:

35315

Cov.:

show subpopulations

Gnomad AFR

AF:

0.675

Gnomad AMI

AF:

0.804

Gnomad AMR

AF:

0.654

Gnomad ASJ

AF:

0.589

Gnomad EAS

AF:

0.596

Gnomad SAS

AF:

0.726

Gnomad FIN

AF:

0.770

Gnomad MID

AF:

0.642

Gnomad NFE

AF:

0.686

Gnomad OTH

AF:

0.651

GnomAD4 exome

AF:

0.684

AC:

886758

AN:

1297288

Hom.:

304109

AF XY:

0.684

AC XY:

436658

AN XY:

638118

show subpopulations

Gnomad4 AFR exome

AF:

0.682

Gnomad4 AMR exome

AF:

0.662

Gnomad4 ASJ exome

AF:

0.584

Gnomad4 EAS exome

AF:

0.578

Gnomad4 SAS exome

AF:

0.729

Gnomad4 FIN exome

AF:

0.764

Gnomad4 NFE exome

AF:

0.684

Gnomad4 OTH exome

AF:

0.680

Alfa

AF:

0.632

Hom.:

1917

Bravo

AF:

0.666

Asia WGS

AF:

0.699

AC:

2435

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1Other:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

This variant is associated with the following publications: (PMID: 27648002, 25992764, 23957473, 25328912, 22993299, 15338501, 11978667, 24205329, 23007030, 16142870, 19653005, 23353010, 10930302, 15963467) -

Microvascular complications of diabetes, susceptibility to, 1

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

May 01, 2002

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

Cadd

Benign

Dann

Benign

0.93

Splicing

Find out SpliceAI 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

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over