12-71930591-G-C

Variant names:

• chr12-71930591-G-C
• rs4131347

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 0.312 in 151,960 control chromosomes in the GnomAD database, including 8,577 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 0.31 (8577 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 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: 0.311 AC: 47288 AN: 151840 Hom.: 8556 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.312 AC: 47355 AN: 151960 Hom.: 8577 Cov.: 32 AF XY: 0.310 AC XY: 23056 AN XY: 74274

African (AFR) AF: 0.473 AC: 19587 AN: 41378

American (AMR) AF: 0.306 AC: 4677 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 823 AN: 3472

East Asian (EAS) AF: 0.549 AC: 2838 AN: 5172

South Asian (SAS) AF: 0.291 AC: 1405 AN: 4822

European-Finnish (FIN) AF: 0.189 AC: 1993 AN: 10560

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15089 AN: 67972

Other (OTH) AF: 0.300 AC: 632 AN: 2106

Alfa AF: 0.122 Hom.: 174

Bravo AF: 0.330

Asia WGS AF: 0.413 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.33
DANN	Benign	0.38
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4131347; hg19: chr12-72324371;