rs1347846

Variant names:

• chr12-90266564-G-A
• rs1347846

Your query was ambiguous. Multiple possible variants found:

• chr12-90266564-G-A
• chr12-90266564-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.329 in 151,856 control chromosomes in the GnomAD database, including 8,314 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 0.33 (8314 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 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: 0.328 AC: 49818 AN: 151736 Hom.: 8297 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.329 AC: 49885 AN: 151856 Hom.: 8314 Cov.: 32 AF XY: 0.334 AC XY: 24814 AN XY: 74246

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.313

Alfa AF: 0.321 Hom.: 10600

Bravo AF: 0.327

Asia WGS AF: 0.424 AC: 1472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.3
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1347846; hg19: chr12-90660341;