rs12085366

Variant names:

• chr1-198447874-T-C
• rs12085366

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 0.158 in 151,854 control chromosomes in the GnomAD database, including 1,999 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 0.16 (1999 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 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: 0.158 AC: 23915 AN: 151736 Hom.: 1996 Cov.: 30

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.158 AC: 23934 AN: 151854 Hom.: 1999 Cov.: 30 AF XY: 0.163 AC XY: 12087 AN XY: 74232

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.167

Alfa AF: 0.150 Hom.: 407

Bravo AF: 0.153

Asia WGS AF: 0.298 AC: 1035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.19
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12085366; hg19: chr1-198417004;