chr10-94991513-T-C

Variant names:

• chr10-94991513-T-C
• rs2185570

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;