rs10488625

Variant names:

• chr7-136593010-A-G
• rs10488625

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 0.207 in 152,052 control chromosomes in the GnomAD database, including 3,748 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 0.21 (3748 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.252 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: 0.207 AC: 31511 AN: 151934 Hom.: 3753 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.0861

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.207 AC: 31498 AN: 152052 Hom.: 3748 Cov.: 32 AF XY: 0.208 AC XY: 15426 AN XY: 74322

African (AFR) AF: 0.108 AC: 4473 AN: 41536

American (AMR) AF: 0.230 AC: 3503 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3468

East Asian (EAS) AF: 0.0861 AC: 446 AN: 5182

South Asian (SAS) AF: 0.239 AC: 1153 AN: 4828

European-Finnish (FIN) AF: 0.260 AC: 2748 AN: 10578

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17298 AN: 67890

Other (OTH) AF: 0.217 AC: 458 AN: 2112

Alfa AF: 0.229 Hom.: 563

Bravo AF: 0.199

Asia WGS AF: 0.182 AC: 631 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.32
PhyloP100		-0.034

Splicing

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

Other links and lift over

dbSNP: rs10488625; hg19: chr7-136277758;