12-108570279-C-T

Variant names:

• chr12-108570279-C-T
• rs741542

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 0.199 in 152,158 control chromosomes in the GnomAD database, including 3,851 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 0.20 (3851 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30241 AN: 152040 Hom.: 3851 Cov.: 32

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.199 AC: 30241 AN: 152158 Hom.: 3851 Cov.: 32 AF XY: 0.205 AC XY: 15242 AN XY: 74380

African (AFR) AF: 0.0473 AC: 1966 AN: 41550

American (AMR) AF: 0.180 AC: 2751 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 662 AN: 3468

East Asian (EAS) AF: 0.489 AC: 2529 AN: 5168

South Asian (SAS) AF: 0.356 AC: 1719 AN: 4828

European-Finnish (FIN) AF: 0.296 AC: 3121 AN: 10558

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.248 AC: 16891 AN: 67988

Other (OTH) AF: 0.205 AC: 431 AN: 2106

Alfa AF: 0.221 Hom.: 2154

Bravo AF: 0.183

Asia WGS AF: 0.398 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.8
DANN	Benign	0.63
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs741542; hg19: chr12-108964055;