rs12134493

chr1-115135325-C-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;