rs6976086

Variant names:

• chr7-15008986-T-G
• rs6976086

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.512 in 129,072 control chromosomes in the GnomAD database, including 14,698 homozygotes. 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: 𝑓 0.51 (14698 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.851
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.512 AC: 66072 AN: 128974 Hom.: 14701 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.546

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.512 AC: 66095 AN: 129072 Hom.: 14698 Cov.: 32 AF XY: 0.521 AC XY: 32643 AN XY: 62688

African (AFR) AF: 0.483 AC: 16295 AN: 33742

American (AMR) AF: 0.601 AC: 7812 AN: 13006

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1615 AN: 3142

East Asian (EAS) AF: 0.362 AC: 1408 AN: 3886

South Asian (SAS) AF: 0.518 AC: 1916 AN: 3698

European-Finnish (FIN) AF: 0.619 AC: 5655 AN: 9140

Middle Eastern (MID) AF: 0.591 AC: 156 AN: 264

European-Non Finnish (NFE) AF: 0.500 AC: 29811 AN: 59592

Other (OTH) AF: 0.539 AC: 954 AN: 1770

Alfa AF: 0.437 Hom.: 24442

Bravo AF: 0.435

Asia WGS AF: 0.323 AC: 1123 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.79
PhyloP100		0.85

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6976086; hg19: chr7-15048611;