rs10505031

Variant names:

• chr8-102587468-T-C
• rs10505031

Your query was ambiguous. Multiple possible variants found:

• chr8-102587468-T-C
• chr8-102587468-T-G

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 0.119 in 152,126 control chromosomes in the GnomAD database, including 1,320 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 0.12 (1320 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.748
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.178 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: 0.119 AC: 18145 AN: 152008 Hom.: 1315 Cov.: 31

Gnomad AFR AF: 0.0457

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0965

Gnomad SAS AF: 0.0885

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.119 AC: 18155 AN: 152126 Hom.: 1320 Cov.: 31 AF XY: 0.123 AC XY: 9122 AN XY: 74368

African (AFR) AF: 0.0456 AC: 1894 AN: 41534

American (AMR) AF: 0.184 AC: 2804 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 653 AN: 3470

East Asian (EAS) AF: 0.0969 AC: 502 AN: 5180

South Asian (SAS) AF: 0.0874 AC: 420 AN: 4808

European-Finnish (FIN) AF: 0.206 AC: 2172 AN: 10558

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9264 AN: 67984

Other (OTH) AF: 0.132 AC: 278 AN: 2112

Alfa AF: 0.126 Hom.: 2639

Bravo AF: 0.116

Asia WGS AF: 0.102 AC: 356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.8
DANN	Benign	0.81
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs10505031; hg19: chr8-103599696;