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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.452

Alfa AF: 0.451 Hom.: 4805

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726402; hg19: chr12-41523709;