rs12724129

chr1-11897582-C-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 0.473 in 151,774 control chromosomes in the GnomAD database, including 17,615 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 0.47 (17615 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71677 AN: 151656 Hom.: 17578 Cov.: 30

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.473 AC: 71779 AN: 151774 Hom.: 17615 Cov.: 30 AF XY: 0.478 AC XY: 35454 AN XY: 74146

Gnomad4 AFR AF: 0.582

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.451

Alfa AF: 0.411 Hom.: 17033

Bravo AF: 0.462

Asia WGS AF: 0.558 AC: 1937 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.5
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12724129; hg19: chr1-11957639;