rs12134493

Variant names:

• chr1-115135325-C-A
• rs12134493

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 35 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0372 AC: 1545 AN: 41560

American (AMR) AF: 0.0988 AC: 1511 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0954 AC: 331 AN: 3468

East Asian (EAS) AF: 0.0772 AC: 400 AN: 5180

South Asian (SAS) AF: 0.102 AC: 491 AN: 4820

European-Finnish (FIN) AF: 0.141 AC: 1490 AN: 10568

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7860 AN: 68002

Other (OTH) AF: 0.0970 AC: 204 AN: 2104

Alfa AF: 0.0855 Hom.: 407

Bravo AF: 0.0854

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	11
DANN	Benign	0.83
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs12134493; hg19: chr1-115677946;