12-119902342-C-G

Variant names:

• chr12-119902342-C-G
• rs6490272

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 0.745 in 152,082 control chromosomes in the GnomAD database, including 42,502 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 0.75 (42502 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.814
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 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: 0.745 AC: 113228 AN: 151964 Hom.: 42454 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.745 AC: 113335 AN: 152082 Hom.: 42502 Cov.: 32 AF XY: 0.752 AC XY: 55937 AN XY: 74346

African (AFR) AF: 0.701 AC: 29071 AN: 41450

American (AMR) AF: 0.771 AC: 11759 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2673 AN: 3468

East Asian (EAS) AF: 0.963 AC: 4988 AN: 5182

South Asian (SAS) AF: 0.822 AC: 3960 AN: 4818

European-Finnish (FIN) AF: 0.795 AC: 8425 AN: 10592

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 50014 AN: 68008

Other (OTH) AF: 0.747 AC: 1577 AN: 2112

Alfa AF: 0.743 Hom.: 5236

Bravo AF: 0.742

Asia WGS AF: 0.876 AC: 3042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.73
DANN	Benign	0.48
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs6490272; hg19: chr12-120340146;