12-20139280-T-C

Variant names:

• chr12-20139280-T-C
• rs977894

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 0.287 in 152,082 control chromosomes in the GnomAD database, including 6,489 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 0.29 (6489 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.82
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 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: 0.287 AC: 43627 AN: 151964 Hom.: 6482 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.287 AC: 43672 AN: 152082 Hom.: 6489 Cov.: 32 AF XY: 0.286 AC XY: 21288 AN XY: 74350

African (AFR) AF: 0.351 AC: 14554 AN: 41458

American (AMR) AF: 0.271 AC: 4145 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 847 AN: 3468

East Asian (EAS) AF: 0.359 AC: 1853 AN: 5160

South Asian (SAS) AF: 0.218 AC: 1052 AN: 4830

European-Finnish (FIN) AF: 0.231 AC: 2441 AN: 10582

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17846 AN: 67978

Other (OTH) AF: 0.320 AC: 675 AN: 2108

Alfa AF: 0.264 Hom.: 3197

Bravo AF: 0.294

Asia WGS AF: 0.254 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.73
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs977894; hg19: chr12-20292214;