8-40973775-A-C

Variant names:

• chr8-40973775-A-C
• rs10094981

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 0.311 in 152,080 control chromosomes in the GnomAD database, including 8,246 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 0.31 (8246 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 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: 0.311 AC: 47217 AN: 151962 Hom.: 8237 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.311 AC: 47258 AN: 152080 Hom.: 8246 Cov.: 32 AF XY: 0.305 AC XY: 22692 AN XY: 74364

African (AFR) AF: 0.479 AC: 19866 AN: 41460

American (AMR) AF: 0.241 AC: 3681 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 867 AN: 3472

East Asian (EAS) AF: 0.239 AC: 1235 AN: 5172

South Asian (SAS) AF: 0.321 AC: 1544 AN: 4816

European-Finnish (FIN) AF: 0.201 AC: 2134 AN: 10592

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17068 AN: 67968

Other (OTH) AF: 0.292 AC: 618 AN: 2114

Alfa AF: 0.263 Hom.: 9052

Bravo AF: 0.320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.1
DANN	Benign	0.49
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs10094981; hg19: chr8-40831294;