rs10085387

Variant names:

• chr7-97759718-A-G
• rs10085387

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;