rs12743074

Variant names:

• chr1-248768834-C-T
• rs12743074

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 0.133 in 152,114 control chromosomes in the GnomAD database, including 1,939 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 0.13 (1939 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 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: 0.133 AC: 20251 AN: 151996 Hom.: 1931 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.0341

Gnomad AMR AF: 0.0643

Gnomad ASJ AF: 0.0982

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.0595

Gnomad FIN AF: 0.0506

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0917

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.133 AC: 20281 AN: 152114 Hom.: 1939 Cov.: 32 AF XY: 0.129 AC XY: 9571 AN XY: 74362

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.0643

Gnomad4 ASJ AF: 0.0982

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.0590

Gnomad4 FIN AF: 0.0506

Gnomad4 NFE AF: 0.0917

Gnomad4 OTH AF: 0.107

Alfa AF: 0.121 Hom.: 189

Bravo AF: 0.140

Asia WGS AF: 0.135 AC: 469 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12743074; hg19: chr1-249063033;