chr12-52681876-T-C

Variant names:

• chr12-52681876-T-C
• rs3759191

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 0.46 in 151,948 control chromosomes in the GnomAD database, including 16,284 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 0.46 (16284 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.585
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.468 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: 0.460 AC: 69824 AN: 151832 Hom.: 16249 Cov.: 31

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.460 AC: 69903 AN: 151948 Hom.: 16284 Cov.: 31 AF XY: 0.456 AC XY: 33840 AN XY: 74244

African (AFR) AF: 0.470 AC: 19467 AN: 41428

American (AMR) AF: 0.425 AC: 6487 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1664 AN: 3468

East Asian (EAS) AF: 0.240 AC: 1242 AN: 5182

South Asian (SAS) AF: 0.474 AC: 2275 AN: 4796

European-Finnish (FIN) AF: 0.467 AC: 4918 AN: 10542

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.473 AC: 32112 AN: 67944

Other (OTH) AF: 0.442 AC: 934 AN: 2114

Alfa AF: 0.475 Hom.: 8954

Bravo AF: 0.455

Asia WGS AF: 0.426 AC: 1481 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	4.1
DANN	Benign	0.39
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs3759191; hg19: chr12-53075660;