rs10958506

Variant names:

• chr8-56868523-A-C
• rs10958506

Your query was ambiguous. Multiple possible variants found:

• chr8-56868523-A-C
• chr8-56868523-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.387 in 152,118 control chromosomes in the GnomAD database, including 12,965 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 0.39 (12965 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 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: 0.387 AC: 58831 AN: 152000 Hom.: 12956 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.387 AC: 58867 AN: 152118 Hom.: 12965 Cov.: 33 AF XY: 0.393 AC XY: 29239 AN XY: 74378

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.394

Alfa AF: 0.409 Hom.: 1687

Bravo AF: 0.386

Asia WGS AF: 0.504 AC: 1749 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10958506; hg19: chr8-57781082;