rs10508324

chr10-7123125-C-Gchr10-7123125-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00445

Gnomad4 AMR AF: 0.0215

Gnomad4 ASJ AF: 0.0358

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.00812

Gnomad4 NFE AF: 0.0204

Gnomad4 OTH AF: 0.0208

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508324; hg19: chr10-7165087;