chr12-19397902-T-C

Variant names:

• chr12-19397902-T-C
• rs2565666

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 0.899 in 151,976 control chromosomes in the GnomAD database, including 61,382 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 0.90 (61382 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.899 AC: 136466 AN: 151858 Hom.: 61336 Cov.: 29

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.830

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.899 AC: 136573 AN: 151976 Hom.: 61382 Cov.: 29 AF XY: 0.901 AC XY: 66927 AN XY: 74284

African (AFR) AF: 0.908 AC: 37627 AN: 41460

American (AMR) AF: 0.917 AC: 13962 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2878 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5123 AN: 5134

South Asian (SAS) AF: 0.860 AC: 4133 AN: 4804

European-Finnish (FIN) AF: 0.929 AC: 9835 AN: 10590

Middle Eastern (MID) AF: 0.824 AC: 239 AN: 290

European-Non Finnish (NFE) AF: 0.884 AC: 60098 AN: 67982

Other (OTH) AF: 0.888 AC: 1868 AN: 2104

Alfa AF: 0.896 Hom.: 12991

Bravo AF: 0.901

Asia WGS AF: 0.934 AC: 3249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.51
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs2565666; hg19: chr12-19550836;