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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

2

Clinical Significance

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

Conservation

PhyloP100: 1.03

Links

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
VEGFANM_003376.6 linkuse as main transcriptc.-94C>G 5_prime_UTR_variant 1/8 ENST00000672860.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
VEGFAENST00000672860.3 linkuse as main transcriptc.-94C>G 5_prime_UTR_variant 1/8 NM_003376.6 P15692-13
ENST00000607600.1 linkuse as main transcriptn.4G>C non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.682
AC:
103572
AN:
151946
Hom.:
35315
Cov.:
33
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 submitterclinical testingGeneDxJun 19, 2021This 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 providedliterature onlyOMIMMay 01, 2002- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
Cadd
Benign
21
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.

Other links and lift over

dbSNP: rs2010963; hg19: chr6-43738350;