rs6960808

Variant names:

• chr7-98031831-C-A
• rs6960808

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 0.456 in 151,338 control chromosomes in the GnomAD database, including 16,847 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 0.46 (16847 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69023 AN: 151222 Hom.: 16837 Cov.: 27

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.456 AC: 69047 AN: 151338 Hom.: 16847 Cov.: 27 AF XY: 0.451 AC XY: 33315 AN XY: 73882

African (AFR) AF: 0.296 AC: 12209 AN: 41284

American (AMR) AF: 0.470 AC: 7125 AN: 15146

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2205 AN: 3464

East Asian (EAS) AF: 0.263 AC: 1331 AN: 5068

South Asian (SAS) AF: 0.498 AC: 2379 AN: 4780

European-Finnish (FIN) AF: 0.456 AC: 4763 AN: 10452

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.551 AC: 37389 AN: 67850

Other (OTH) AF: 0.500 AC: 1046 AN: 2094

Alfa AF: 0.529 Hom.: 69512

Bravo AF: 0.452

Asia WGS AF: 0.387 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.73
PhyloP100		0.052

Splicing

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

Other links and lift over

dbSNP: rs6960808; hg19: chr7-97661143;