rs221657

Variant names:

• chr6-105100975-C-G
• rs221657
• NM_001199563.2:c.*114G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-105100975-C-G
• chr6-105100975-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134

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]

ACMG classification

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
BVES	NM_001199563.2	c.*114G>C		3_prime_UTR_variant	Exon 8 of 8	ENST00000314641.10	NP_001186492.1
BVES	NM_007073.4	c.*114G>C		3_prime_UTR_variant	Exon 8 of 8		NP_009004.2
BVES	NM_147147.4	c.*114G>C		3_prime_UTR_variant	Exon 8 of 8		NP_671488.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BVES	ENST00000314641	c.*114G>C		3_prime_UTR_variant	Exon 8 of 8	1	NM_001199563.2	ENSP00000313172.5
BVES	ENST00000336775	c.*114G>C		3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000337259.5
BVES	ENST00000446408	c.*114G>C		3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000397310.2

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

Other links and lift over

dbSNP: rs221657; hg19: chr6-105548850;