8-58500631-A-G

Variant names:

• chr8-58500631-A-G
• rs3824260

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 0.572 in 151,882 control chromosomes in the GnomAD database, including 25,171 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 0.57 (25171 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86808 AN: 151762 Hom.: 25149 Cov.: 31

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.572 AC: 86866 AN: 151882 Hom.: 25171 Cov.: 31 AF XY: 0.569 AC XY: 42197 AN XY: 74224

African (AFR) AF: 0.503 AC: 20848 AN: 41418

American (AMR) AF: 0.672 AC: 10266 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2265 AN: 3460

East Asian (EAS) AF: 0.538 AC: 2780 AN: 5164

South Asian (SAS) AF: 0.567 AC: 2737 AN: 4826

European-Finnish (FIN) AF: 0.486 AC: 5132 AN: 10550

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.602 AC: 40863 AN: 67880

Other (OTH) AF: 0.584 AC: 1233 AN: 2110

Alfa AF: 0.597 Hom.: 45493

Bravo AF: 0.582

Asia WGS AF: 0.563 AC: 1956 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.1
DANN	Benign	0.64
PhyloP100		0.20
PromoterAI		-0.0076	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3824260; hg19: chr8-59413190; COSMIC: COSV56962695;