rs726402

Variant names:

• chr12-41129907-A-G
• rs726402

Your query was ambiguous. Multiple possible variants found:

• chr12-41129907-A-G
• chr12-41129907-A-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 0.475 in 151,668 control chromosomes in the GnomAD database, including 17,498 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 0.48 (17498 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.56 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: 0.475 AC: 72013 AN: 151550 Hom.: 17477 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.475 AC: 72079 AN: 151668 Hom.: 17498 Cov.: 32 AF XY: 0.475 AC XY: 35205 AN XY: 74124

African (AFR) AF: 0.566 AC: 23450 AN: 41402

American (AMR) AF: 0.410 AC: 6239 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1617 AN: 3468

East Asian (EAS) AF: 0.397 AC: 2028 AN: 5114

South Asian (SAS) AF: 0.365 AC: 1760 AN: 4818

European-Finnish (FIN) AF: 0.498 AC: 5244 AN: 10530

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.448 AC: 30400 AN: 67806

Other (OTH) AF: 0.452 AC: 950 AN: 2102

Alfa AF: 0.452 Hom.: 6001

Bravo AF: 0.474

Asia WGS AF: 0.391 AC: 1361 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.49
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs726402; hg19: chr12-41523709;