rs56260627

Variant names:

• chr12-34098266-G-A
• rs56260627

Your query was ambiguous. Multiple possible variants found:

• chr12-34098266-G-A
• chr12-34098266-G-C

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 0.0675 in 152,278 control chromosomes in the GnomAD database, including 467 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 0.067 (467 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 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: 0.0675 AC: 10272 AN: 152160 Hom.: 467 Cov.: 32

Gnomad AFR AF: 0.0178

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0567

Gnomad ASJ AF: 0.0619

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.00993

Gnomad FIN AF: 0.0729

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0675 AC: 10274 AN: 152278 Hom.: 467 Cov.: 32 AF XY: 0.0642 AC XY: 4783 AN XY: 74466

African (AFR) AF: 0.0177 AC: 737 AN: 41566

American (AMR) AF: 0.0566 AC: 866 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0619 AC: 215 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5186

South Asian (SAS) AF: 0.0104 AC: 50 AN: 4828

European-Finnish (FIN) AF: 0.0729 AC: 773 AN: 10602

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7341 AN: 68014

Other (OTH) AF: 0.0672 AC: 142 AN: 2112

Alfa AF: 0.0863 Hom.: 843

Bravo AF: 0.0645

Asia WGS AF: 0.00895 AC: 31 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.58
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs56260627; hg19: chr12-34251201;