rs12246561

Variant names:

• chr10-111075351-A-C
• rs12246561

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0878 in 152,284 control chromosomes in the GnomAD database, including 632 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 (632 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.095 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: 0.0878 AC: 13353 AN: 152166 Hom.: 626 Cov.: 33

Gnomad AFR AF: 0.0708

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0741

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0535

Gnomad SAS AF: 0.0944

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0969

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0878 AC: 13374 AN: 152284 Hom.: 632 Cov.: 33 AF XY: 0.0884 AC XY: 6583 AN XY: 74458

African (AFR) AF: 0.0709 AC: 2944 AN: 41548

American (AMR) AF: 0.0740 AC: 1133 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 490 AN: 3472

East Asian (EAS) AF: 0.0532 AC: 276 AN: 5184

South Asian (SAS) AF: 0.0940 AC: 454 AN: 4828

European-Finnish (FIN) AF: 0.103 AC: 1092 AN: 10606

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.0969 AC: 6594 AN: 68018

Other (OTH) AF: 0.114 AC: 241 AN: 2114

Alfa AF: 0.0945 Hom.: 952

Bravo AF: 0.0860

Asia WGS AF: 0.104 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.70
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs12246561; hg19: chr10-112835109;