chr8-58476006-T-C

Variant names:

• chr8-58476006-T-C
• rs2081687

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 0.695 in 152,102 control chromosomes in the GnomAD database, including 36,955 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 0.70 (36955 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 81 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 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: 0.695 AC: 105667 AN: 151982 Hom.: 36919 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.695 AC: 105756 AN: 152102 Hom.: 36955 Cov.: 32 AF XY: 0.694 AC XY: 51582 AN XY: 74346

African (AFR) AF: 0.754 AC: 31294 AN: 41494

American (AMR) AF: 0.762 AC: 11646 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2395 AN: 3470

East Asian (EAS) AF: 0.783 AC: 4049 AN: 5172

South Asian (SAS) AF: 0.668 AC: 3222 AN: 4822

European-Finnish (FIN) AF: 0.604 AC: 6378 AN: 10560

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44502 AN: 67990

Other (OTH) AF: 0.696 AC: 1465 AN: 2104

Alfa AF: 0.672 Hom.: 104339

Bravo AF: 0.712

Asia WGS AF: 0.724 AC: 2516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.64
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs2081687; hg19: chr8-59388565;