rs2185570

Positions:

• chr10-94991513-T-C

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 0.0882 in 152,148 control chromosomes in the GnomAD database, including 759 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 0.088 (759 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 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: 0.0883 AC: 13428 AN: 152030 Hom.: 759 Cov.: 32

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0978

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0395

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0882 AC: 13423 AN: 152148 Hom.: 759 Cov.: 32 AF XY: 0.0871 AC XY: 6482 AN XY: 74400

Gnomad4 AFR AF: 0.0235

Gnomad4 AMR AF: 0.0976

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0395

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.111

Alfa AF: 0.102 Hom.: 90

Bravo AF: 0.0859

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2185570; hg19: chr10-96751270;