rs4931594

Variant names:

• chr12-31997309-A-C
• rs4931594

Your query was ambiguous. Multiple possible variants found:

• chr12-31997309-A-C
• chr12-31997309-A-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 0.144 in 151,652 control chromosomes in the GnomAD database, including 1,848 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 (1848 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.206 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: 0.144 AC: 21847 AN: 151534 Hom.: 1849 Cov.: 31

Gnomad AFR AF: 0.0513

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.144 AC: 21846 AN: 151652 Hom.: 1848 Cov.: 31 AF XY: 0.147 AC XY: 10923 AN XY: 74148

African (AFR) AF: 0.0512 AC: 2112 AN: 41276

American (AMR) AF: 0.212 AC: 3222 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 530 AN: 3468

East Asian (EAS) AF: 0.155 AC: 794 AN: 5124

South Asian (SAS) AF: 0.175 AC: 841 AN: 4810

European-Finnish (FIN) AF: 0.201 AC: 2119 AN: 10558

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11676 AN: 67900

Other (OTH) AF: 0.139 AC: 292 AN: 2102

Alfa AF: 0.146 Hom.: 2372

Bravo AF: 0.140

Asia WGS AF: 0.140 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.9
DANN	Benign	0.36
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4931594; hg19: chr12-32150243;