rs10508558

Variant names:

• chr10-18099505-A-C
• rs10508558

Your query was ambiguous. Multiple possible variants found:

• chr10-18099505-A-C
• chr10-18099505-A-T

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 0.0948 in 152,206 control chromosomes in the GnomAD database, including 934 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 0.095 (934 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 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: 0.0947 AC: 14408 AN: 152090 Hom.: 932 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0799

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0475

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0561

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.0948 AC: 14432 AN: 152206 Hom.: 934 Cov.: 32 AF XY: 0.0966 AC XY: 7190 AN XY: 74410

African (AFR) AF: 0.147 AC: 6099 AN: 41516

American (AMR) AF: 0.0798 AC: 1220 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0899 AC: 312 AN: 3472

East Asian (EAS) AF: 0.332 AC: 1716 AN: 5170

South Asian (SAS) AF: 0.105 AC: 504 AN: 4822

European-Finnish (FIN) AF: 0.0475 AC: 504 AN: 10604

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0562 AC: 3819 AN: 68010

Other (OTH) AF: 0.0919 AC: 194 AN: 2112

Alfa AF: 0.0740 Hom.: 1994

Bravo AF: 0.101

Asia WGS AF: 0.256 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.45
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10508558; hg19: chr10-18388434;