rs10085387

chr7-97759718-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 0.238 in 152,154 control chromosomes in the GnomAD database, including 4,502 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 0.24 (4502 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 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: 0.238 AC: 36260 AN: 152036 Hom.: 4496 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0880

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.238 AC: 36280 AN: 152154 Hom.: 4502 Cov.: 31 AF XY: 0.233 AC XY: 17349 AN XY: 74404

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.0882

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.217

Alfa AF: 0.257 Hom.: 6772

Bravo AF: 0.233

Asia WGS AF: 0.119 AC: 412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	4.3
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10085387; hg19: chr7-97389030;