rs10515822

Variant names:

• chr5-161153087-C-T
• rs10515822

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 0.0963 in 151,932 control chromosomes in the GnomAD database, including 833 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 0.096 (833 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.2 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: 0.0962 AC: 14607 AN: 151814 Hom.: 830 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0743

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.0368

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0767

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0963 AC: 14633 AN: 151932 Hom.: 833 Cov.: 32 AF XY: 0.0975 AC XY: 7243 AN XY: 74252

African (AFR) AF: 0.125 AC: 5200 AN: 41456

American (AMR) AF: 0.0744 AC: 1136 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 397 AN: 3460

East Asian (EAS) AF: 0.188 AC: 965 AN: 5120

South Asian (SAS) AF: 0.211 AC: 1017 AN: 4814

European-Finnish (FIN) AF: 0.0368 AC: 390 AN: 10586

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.0767 AC: 5208 AN: 67920

Other (OTH) AF: 0.105 AC: 221 AN: 2110

Alfa AF: 0.0909 Hom.: 541

Bravo AF: 0.0978

Asia WGS AF: 0.181 AC: 627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.69
PhyloP100		0.050

Splicing

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

Other links and lift over

dbSNP: rs10515822; hg19: chr5-160580094;