chr8-58508057-G-C

Variant names:

• chr8-58508057-G-C
• rs1023652

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 0.671 in 151,958 control chromosomes in the GnomAD database, including 34,950 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 0.67 (34950 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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: 0.671 AC: 101902 AN: 151840 Hom.: 34908 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.671 AC: 102000 AN: 151958 Hom.: 34950 Cov.: 31 AF XY: 0.669 AC XY: 49673 AN XY: 74248

African (AFR) AF: 0.819 AC: 33961 AN: 41448

American (AMR) AF: 0.727 AC: 11107 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2165 AN: 3470

East Asian (EAS) AF: 0.633 AC: 3267 AN: 5162

South Asian (SAS) AF: 0.602 AC: 2895 AN: 4810

European-Finnish (FIN) AF: 0.564 AC: 5947 AN: 10538

Middle Eastern (MID) AF: 0.640 AC: 187 AN: 292

European-Non Finnish (NFE) AF: 0.597 AC: 40564 AN: 67950

Other (OTH) AF: 0.659 AC: 1390 AN: 2108

Alfa AF: 0.468 Hom.: 1104

Bravo AF: 0.691

Asia WGS AF: 0.625 AC: 2173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.8
DANN	Benign	0.74
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1023652; hg19: chr8-59420616;