rs1696422

Variant names:

• chr12-130083645-G-A
• rs1696422

Your query was ambiguous. Multiple possible variants found:

• chr12-130083645-G-A
• chr12-130083645-G-T

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 0.318 in 151,924 control chromosomes in the GnomAD database, including 8,044 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 0.32 (8044 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.435 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: 0.318 AC: 48305 AN: 151806 Hom.: 8022 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.318 AC: 48364 AN: 151924 Hom.: 8044 Cov.: 32 AF XY: 0.325 AC XY: 24130 AN XY: 74264

African (AFR) AF: 0.291 AC: 12065 AN: 41416

American (AMR) AF: 0.441 AC: 6729 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1097 AN: 3462

East Asian (EAS) AF: 0.391 AC: 2010 AN: 5142

South Asian (SAS) AF: 0.451 AC: 2163 AN: 4798

European-Finnish (FIN) AF: 0.311 AC: 3281 AN: 10558

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19970 AN: 67980

Other (OTH) AF: 0.345 AC: 727 AN: 2106

Alfa AF: 0.305 Hom.: 12079

Bravo AF: 0.326

Asia WGS AF: 0.419 AC: 1457 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	0.085
DANN	Benign	0.47
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1696422; hg19: chr12-130568190; COSMIC: COSV68527030;