rs12120353

Variant names:

• chr1-4560936-C-A
• rs12120353

Your query was ambiguous. Multiple possible variants found:

• chr1-4560936-C-A
• chr1-4560936-C-T

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 0.207 in 152,026 control chromosomes in the GnomAD database, including 3,380 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 0.21 (3380 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.224 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: 0.207 AC: 31511 AN: 151908 Hom.: 3381 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.207 AC: 31522 AN: 152026 Hom.: 3380 Cov.: 32 AF XY: 0.209 AC XY: 15527 AN XY: 74310

African (AFR) AF: 0.197 AC: 8154 AN: 41466

American (AMR) AF: 0.169 AC: 2583 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 913 AN: 3466

East Asian (EAS) AF: 0.0111 AC: 57 AN: 5152

South Asian (SAS) AF: 0.235 AC: 1129 AN: 4804

European-Finnish (FIN) AF: 0.254 AC: 2682 AN: 10570

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15208 AN: 67966

Other (OTH) AF: 0.195 AC: 413 AN: 2114

Alfa AF: 0.214 Hom.: 15152

Bravo AF: 0.200

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.15
DANN	Benign	0.44
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs12120353; hg19: chr1-4620996; COSMIC: COSV59920009;