chr11-82738676-G-A

Variant names:

• chr11-82738676-G-A
• rs9665943

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.421 in 151,872 control chromosomes in the GnomAD database, including 17,430 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 0.42 (17430 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63846 AN: 151754 Hom.: 17377 Cov.: 32

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.407

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.421 AC: 63971 AN: 151872 Hom.: 17430 Cov.: 32 AF XY: 0.418 AC XY: 31004 AN XY: 74208

African (AFR) AF: 0.773 AC: 32069 AN: 41466

American (AMR) AF: 0.343 AC: 5230 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 910 AN: 3470

East Asian (EAS) AF: 0.534 AC: 2758 AN: 5162

South Asian (SAS) AF: 0.368 AC: 1767 AN: 4802

European-Finnish (FIN) AF: 0.234 AC: 2459 AN: 10512

Middle Eastern (MID) AF: 0.421 AC: 122 AN: 290

European-Non Finnish (NFE) AF: 0.260 AC: 17649 AN: 67906

Other (OTH) AF: 0.400 AC: 841 AN: 2104

Alfa AF: 0.310 Hom.: 11160

Bravo AF: 0.443

Asia WGS AF: 0.456 AC: 1586 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	11
DANN	Benign	0.68
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs9665943; hg19: chr11-82449718;