rs10508324

Variant names:

• chr10-7123125-C-G
• rs10508324

Your query was ambiguous. Multiple possible variants found:

• chr10-7123125-C-G
• chr10-7123125-C-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 0.0238 in 152,218 control chromosomes in the GnomAD database, including 165 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 0.024 (165 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.673
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.167 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: 0.0238 AC: 3621 AN: 152100 Hom.: 166 Cov.: 32

Gnomad AFR AF: 0.00447

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0216

Gnomad ASJ AF: 0.0358

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.00812

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0204

Gnomad OTH AF: 0.0210

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

GnomAD4 genome AF: 0.0238 AC: 3616 AN: 152218 Hom.: 165 Cov.: 32 AF XY: 0.0255 AC XY: 1900 AN XY: 74406

African (AFR) AF: 0.00445 AC: 185 AN: 41540

American (AMR) AF: 0.0215 AC: 329 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0358 AC: 124 AN: 3466

East Asian (EAS) AF: 0.177 AC: 915 AN: 5180

South Asian (SAS) AF: 0.112 AC: 537 AN: 4816

European-Finnish (FIN) AF: 0.00812 AC: 86 AN: 10590

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0204 AC: 1389 AN: 68026

Other (OTH) AF: 0.0208 AC: 44 AN: 2114

Alfa AF: 0.0165 Hom.: 6

Bravo AF: 0.0228

Asia WGS AF: 0.118 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.58
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs10508324; hg19: chr10-7165087;