rs10488625

Positions:

• chr7-136593010-A-G

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 0.207 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.0861

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.217

Alfa AF: 0.234 Hom.: 560

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488625; hg19: chr7-136277758;