chr12-41780629-C-T

Variant names:

• chr12-41780629-C-T
• rs10880160

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 0.346 in 151,948 control chromosomes in the GnomAD database, including 9,942 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 0.35 (9942 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 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: 0.346 AC: 52506 AN: 151832 Hom.: 9916 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.346 AC: 52579 AN: 151948 Hom.: 9942 Cov.: 32 AF XY: 0.345 AC XY: 25661 AN XY: 74288

African (AFR) AF: 0.501 AC: 20738 AN: 41418

American (AMR) AF: 0.270 AC: 4115 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 720 AN: 3468

East Asian (EAS) AF: 0.297 AC: 1529 AN: 5148

South Asian (SAS) AF: 0.266 AC: 1277 AN: 4808

European-Finnish (FIN) AF: 0.314 AC: 3316 AN: 10562

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 20016 AN: 67972

Other (OTH) AF: 0.310 AC: 653 AN: 2104

Alfa AF: 0.305 Hom.: 23143

Bravo AF: 0.343

Asia WGS AF: 0.266 AC: 924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.65
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs10880160; hg19: chr12-42174431;