8-56909681-T-C

Variant names:

• chr8-56909681-T-C
• rs985942

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 0.603 in 152,134 control chromosomes in the GnomAD database, including 28,196 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 0.60 (28196 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 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: 0.603 AC: 91593 AN: 152016 Hom.: 28161 Cov.: 33

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.603 AC: 91685 AN: 152134 Hom.: 28196 Cov.: 33 AF XY: 0.606 AC XY: 45089 AN XY: 74360

African (AFR) AF: 0.684 AC: 28368 AN: 41490

American (AMR) AF: 0.587 AC: 8972 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1860 AN: 3472

East Asian (EAS) AF: 0.795 AC: 4110 AN: 5168

South Asian (SAS) AF: 0.525 AC: 2531 AN: 4822

European-Finnish (FIN) AF: 0.655 AC: 6932 AN: 10590

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37193 AN: 67976

Other (OTH) AF: 0.584 AC: 1235 AN: 2116

Alfa AF: 0.590 Hom.: 4372

Bravo AF: 0.607

Asia WGS AF: 0.656 AC: 2278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.65
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs985942; hg19: chr8-57822240;