chr6-105116015-C-A

Variant summary

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

The NM_001199563.2(BVES):​c.817-188G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 152,074 control chromosomes in the GnomAD database, including 51,501 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.82 ( 51501 hom., cov: 32)

Consequence

BVES
NM_001199563.2 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.00300
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 Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 6-105116015-C-A is Benign according to our data. Variant chr6-105116015-C-A is described in ClinVar as [Benign]. Clinvar id is 1288486.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BVESNM_001199563.2 linkuse as main transcriptc.817-188G>T intron_variant ENST00000314641.10 NP_001186492.1 Q8NE79
BVESNM_007073.4 linkuse as main transcriptc.817-188G>T intron_variant NP_009004.2 Q8NE79
BVESNM_147147.4 linkuse as main transcriptc.817-188G>T intron_variant NP_671488.1 Q8NE79

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BVESENST00000314641.10 linkuse as main transcriptc.817-188G>T intron_variant 1 NM_001199563.2 ENSP00000313172.5 Q8NE79
BVESENST00000336775.9 linkuse as main transcriptc.817-188G>T intron_variant 1 ENSP00000337259.5 Q8NE79
BVESENST00000446408.2 linkuse as main transcriptc.817-188G>T intron_variant 1 ENSP00000397310.2 Q8NE79

Frequencies

GnomAD3 genomes
AF:
0.816
AC:
124036
AN:
151956
Hom.:
51481
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.649
Gnomad AMI
AF:
0.963
Gnomad AMR
AF:
0.874
Gnomad ASJ
AF:
0.841
Gnomad EAS
AF:
0.867
Gnomad SAS
AF:
0.837
Gnomad FIN
AF:
0.904
Gnomad MID
AF:
0.728
Gnomad NFE
AF:
0.883
Gnomad OTH
AF:
0.819
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.816
AC:
124102
AN:
152074
Hom.:
51501
Cov.:
32
AF XY:
0.817
AC XY:
60743
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.649
Gnomad4 AMR
AF:
0.874
Gnomad4 ASJ
AF:
0.841
Gnomad4 EAS
AF:
0.867
Gnomad4 SAS
AF:
0.837
Gnomad4 FIN
AF:
0.904
Gnomad4 NFE
AF:
0.883
Gnomad4 OTH
AF:
0.820
Alfa
AF:
0.821
Hom.:
5584
Bravo
AF:
0.806
Asia WGS
AF:
0.849
AC:
2936
AN:
3456

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJul 06, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.68
DANN
Benign
0.18

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: rs1318746; hg19: chr6-105563890; API