rs6982753

Variant names:

• chr8-42749648-A-G
• rs6982753

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 0.35 in 152,174 control chromosomes in the GnomAD database, including 13,675 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 0.35 (13675 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.05
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 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: 0.350 AC: 53177 AN: 152056 Hom.: 13625 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.350 AC: 53286 AN: 152174 Hom.: 13675 Cov.: 32 AF XY: 0.344 AC XY: 25626 AN XY: 74390

African (AFR) AF: 0.729 AC: 30224 AN: 41480

American (AMR) AF: 0.272 AC: 4152 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 767 AN: 3472

East Asian (EAS) AF: 0.214 AC: 1107 AN: 5184

South Asian (SAS) AF: 0.204 AC: 987 AN: 4828

European-Finnish (FIN) AF: 0.184 AC: 1952 AN: 10596

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.195 AC: 13267 AN: 68010

Other (OTH) AF: 0.319 AC: 676 AN: 2116

Alfa AF: 0.244 Hom.: 7633

Bravo AF: 0.375

Asia WGS AF: 0.270 AC: 941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.032
DANN	Benign	0.17
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs6982753; hg19: chr8-42604791;