rs12412561

Variant names:

• chr10-53409781-T-C
• rs12412561

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 0.112 in 151,946 control chromosomes in the GnomAD database, including 1,264 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 0.11 (1264 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 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: 0.112 AC: 16998 AN: 151828 Hom.: 1263 Cov.: 32

Gnomad AFR AF: 0.0316

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0711

Gnomad EAS AF: 0.00443

Gnomad SAS AF: 0.0944

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.112 AC: 16996 AN: 151946 Hom.: 1264 Cov.: 32 AF XY: 0.110 AC XY: 8198 AN XY: 74248

African (AFR) AF: 0.0315 AC: 1307 AN: 41506

American (AMR) AF: 0.115 AC: 1749 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.0711 AC: 246 AN: 3460

East Asian (EAS) AF: 0.00444 AC: 23 AN: 5176

South Asian (SAS) AF: 0.0947 AC: 457 AN: 4824

European-Finnish (FIN) AF: 0.183 AC: 1943 AN: 10592

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 10985 AN: 67874

Other (OTH) AF: 0.107 AC: 226 AN: 2108

Alfa AF: 0.137 Hom.: 5021

Bravo AF: 0.101

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.66
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs12412561; hg19: chr10-55169541;