12-14029992-C-T

Variant names:

• chr12-14029992-C-T
• rs1861872

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 0.861 in 152,166 control chromosomes in the GnomAD database, including 57,067 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 0.86 (57067 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130976 AN: 152048 Hom.: 57033 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.861 AC: 131062 AN: 152166 Hom.: 57067 Cov.: 32 AF XY: 0.858 AC XY: 63838 AN XY: 74396

African (AFR) AF: 0.751 AC: 31165 AN: 41490

American (AMR) AF: 0.903 AC: 13817 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.904 AC: 3138 AN: 3472

East Asian (EAS) AF: 0.644 AC: 3326 AN: 5164

South Asian (SAS) AF: 0.822 AC: 3967 AN: 4826

European-Finnish (FIN) AF: 0.901 AC: 9550 AN: 10602

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.928 AC: 63113 AN: 67998

Other (OTH) AF: 0.863 AC: 1823 AN: 2112

Alfa AF: 0.905 Hom.: 195304

Bravo AF: 0.858

Asia WGS AF: 0.738 AC: 2568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.57
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs1861872; hg19: chr12-14182926;