rs221657

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001199563.2(BVES):​c.*114G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)

Consequence

BVES
NM_001199563.2 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.134
Variant links:
Genes affected
BVES (HGNC:1152): (blood vessel epicardial substance) This gene encodes a member of the POP family of proteins containing three putative transmembrane domains. This gene is expressed in cardiac and skeletal muscle and may play an important role in development of these tissues. The mouse ortholog may be involved in the regeneration of adult skeletal muscle and may act as a cell adhesion molecule in coronary vasculogenesis. Three transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Dec 2010]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BVESNM_001199563.2 linkc.*114G>C 3_prime_UTR_variant Exon 8 of 8 ENST00000314641.10 NP_001186492.1 Q8NE79
BVESNM_007073.4 linkc.*114G>C 3_prime_UTR_variant Exon 8 of 8 NP_009004.2 Q8NE79
BVESNM_147147.4 linkc.*114G>C 3_prime_UTR_variant Exon 8 of 8 NP_671488.1 Q8NE79

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BVESENST00000314641 linkc.*114G>C 3_prime_UTR_variant Exon 8 of 8 1 NM_001199563.2 ENSP00000313172.5 Q8NE79
BVESENST00000336775 linkc.*114G>C 3_prime_UTR_variant Exon 8 of 8 1 ENSP00000337259.5 Q8NE79
BVESENST00000446408 linkc.*114G>C 3_prime_UTR_variant Exon 8 of 8 1 ENSP00000397310.2 Q8NE79

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
14
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
0.48
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.

Other links and lift over

dbSNP: rs221657; hg19: chr6-105548850; API