rs12093061

chr1-231433945-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 0.51 in 152,090 control chromosomes in the GnomAD database, including 21,302 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 0.51 (21302 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.716 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: 0.510 AC: 77470 AN: 151972 Hom.: 21248 Cov.: 33

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.510 AC: 77577 AN: 152090 Hom.: 21302 Cov.: 33 AF XY: 0.503 AC XY: 37379 AN XY: 74342

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.499

Alfa AF: 0.445 Hom.: 15892

Bravo AF: 0.540

Asia WGS AF: 0.508 AC: 1771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	7.9
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12093061; hg19: chr1-231569691;