rs12134493

Variant names:

• chr1-115135325-C-A
• rs12134493

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 0.0921 in 152,194 control chromosomes in the GnomAD database, including 756 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 0.092 (756 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.113 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: 0.0922 AC: 14021 AN: 152076 Hom.: 756 Cov.: 32

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.0990

Gnomad ASJ AF: 0.0954

Gnomad EAS AF: 0.0770

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0980

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

GnomAD4 genome AF: 0.0921 AC: 14019 AN: 152194 Hom.: 756 Cov.: 32 AF XY: 0.0948 AC XY: 7055 AN XY: 74394

Gnomad4 AFR AF: 0.0372

Gnomad4 AMR AF: 0.0988

Gnomad4 ASJ AF: 0.0954

Gnomad4 EAS AF: 0.0772

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.0970

Alfa AF: 0.0962 Hom.: 130

Bravo AF: 0.0854

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	11
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12134493; hg19: chr1-115677946;