rs4131348

Variant names:

• chr12-71930699-T-C
• rs4131348

Your query was ambiguous. Multiple possible variants found:

• chr12-71930699-T-C
• chr12-71930699-T-G

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 0.137 in 152,132 control chromosomes in the GnomAD database, including 1,751 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 0.14 (1751 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 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: 0.137 AC: 20834 AN: 152014 Hom.: 1755 Cov.: 32

Gnomad AFR AF: 0.0735

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.137 AC: 20823 AN: 152132 Hom.: 1751 Cov.: 32 AF XY: 0.137 AC XY: 10188 AN XY: 74370

African (AFR) AF: 0.0735 AC: 3051 AN: 41532

American (AMR) AF: 0.178 AC: 2722 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 683 AN: 3470

East Asian (EAS) AF: 0.366 AC: 1892 AN: 5164

South Asian (SAS) AF: 0.162 AC: 784 AN: 4826

European-Finnish (FIN) AF: 0.113 AC: 1197 AN: 10586

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.146 AC: 9938 AN: 67976

Other (OTH) AF: 0.153 AC: 322 AN: 2106

Alfa AF: 0.146 Hom.: 859

Bravo AF: 0.142

Asia WGS AF: 0.213 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	10
DANN	Benign	0.56
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs4131348; hg19: chr12-72324479;