rs12134279

Variant names:

• chr1-197812068-C-T
• rs12134279

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 0.174 in 152,082 control chromosomes in the GnomAD database, including 2,603 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 0.17 (2603 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 44 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.22 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: 0.174 AC: 26450 AN: 151964 Hom.: 2604 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.174 AC: 26454 AN: 152082 Hom.: 2603 Cov.: 31 AF XY: 0.171 AC XY: 12747 AN XY: 74352

African (AFR) AF: 0.110 AC: 4547 AN: 41494

American (AMR) AF: 0.184 AC: 2808 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 587 AN: 3468

East Asian (EAS) AF: 0.206 AC: 1065 AN: 5160

South Asian (SAS) AF: 0.231 AC: 1112 AN: 4812

European-Finnish (FIN) AF: 0.134 AC: 1412 AN: 10576

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.210 AC: 14301 AN: 67976

Other (OTH) AF: 0.198 AC: 417 AN: 2110

Alfa AF: 0.198 Hom.: 12712

Bravo AF: 0.171

Asia WGS AF: 0.262 AC: 906 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.38
PhyloP100		0.069

Splicing

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

Other links and lift over

dbSNP: rs12134279; hg19: chr1-197781198; COSMIC: COSV60014292;