rs10509155

Variant names:

• chr10-61642160-A-G
• rs10509155

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0247 in 152,184 control chromosomes in the GnomAD database, including 160 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 0.025 (160 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.87
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 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: 0.0247 AC: 3761 AN: 152066 Hom.: 160 Cov.: 32

Gnomad AFR AF: 0.00645

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0296

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0474

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0184

Gnomad OTH AF: 0.0196

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

GnomAD4 genome AF: 0.0247 AC: 3756 AN: 152184 Hom.: 160 Cov.: 32 AF XY: 0.0271 AC XY: 2017 AN XY: 74408

African (AFR) AF: 0.00643 AC: 267 AN: 41546

American (AMR) AF: 0.0295 AC: 450 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 52 AN: 3472

East Asian (EAS) AF: 0.209 AC: 1081 AN: 5170

South Asian (SAS) AF: 0.0238 AC: 115 AN: 4830

European-Finnish (FIN) AF: 0.0474 AC: 501 AN: 10572

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0184 AC: 1248 AN: 67996

Other (OTH) AF: 0.0189 AC: 40 AN: 2114

Alfa AF: 0.0209 Hom.: 7

Bravo AF: 0.0252

Asia WGS AF: 0.105 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	14
DANN	Benign	0.72
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs10509155; hg19: chr10-63401918;