rs12724129

Variant names:

• chr1-11897582-C-T
• rs12724129

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;