rs12356435

Variant names:

• chr10-10094510-G-A
• rs12356435

Your query was ambiguous. Multiple possible variants found:

• chr10-10094510-G-A
• chr10-10094510-G-T

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 0.237 in 152,086 control chromosomes in the GnomAD database, including 5,389 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 (5389 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 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: 0.237 AC: 35970 AN: 151968 Hom.: 5387 Cov.: 33

Gnomad AFR AF: 0.0918

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.00751

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.237 AC: 35972 AN: 152086 Hom.: 5389 Cov.: 33 AF XY: 0.240 AC XY: 17826 AN XY: 74356

Gnomad4 AFR AF: 0.0918

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.00752

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.222

Alfa AF: 0.288 Hom.: 9847

Bravo AF: 0.212

Asia WGS AF: 0.127 AC: 444 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12356435; hg19: chr10-10136473;