12-41811527-C-T

Variant names:

• chr12-41811527-C-T
• rs11532502

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 0.129 in 152,008 control chromosomes in the GnomAD database, including 1,607 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 0.13 (1607 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.18 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: 0.129 AC: 19659 AN: 151890 Hom.: 1610 Cov.: 32

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0567

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.129 AC: 19643 AN: 152008 Hom.: 1607 Cov.: 32 AF XY: 0.131 AC XY: 9703 AN XY: 74314

African (AFR) AF: 0.0323 AC: 1340 AN: 41478

American (AMR) AF: 0.118 AC: 1805 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3470

East Asian (EAS) AF: 0.0568 AC: 294 AN: 5174

South Asian (SAS) AF: 0.156 AC: 751 AN: 4820

European-Finnish (FIN) AF: 0.199 AC: 2105 AN: 10566

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12428 AN: 67936

Other (OTH) AF: 0.131 AC: 276 AN: 2110

Alfa AF: 0.103 Hom.: 246

Bravo AF: 0.116

Asia WGS AF: 0.107 AC: 370 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	2.0
DANN	Benign	0.66
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs11532502; hg19: chr12-42205329;