chr12-42859612-T-G

Variant names:

• chr12-42859612-T-G
• rs1520832

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 0.971 in 152,338 control chromosomes in the GnomAD database, including 71,879 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 0.97 (71879 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.983 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: 0.971 AC: 147822 AN: 152220 Hom.: 71822 Cov.: 33

Gnomad AFR AF: 0.991

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.951

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.973

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

GnomAD4 genome AF: 0.971 AC: 147938 AN: 152338 Hom.: 71879 Cov.: 33 AF XY: 0.971 AC XY: 72288 AN XY: 74478

African (AFR) AF: 0.991 AC: 41196 AN: 41590

American (AMR) AF: 0.971 AC: 14860 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.951 AC: 3303 AN: 3472

East Asian (EAS) AF: 0.871 AC: 4501 AN: 5170

South Asian (SAS) AF: 0.958 AC: 4625 AN: 4830

European-Finnish (FIN) AF: 0.979 AC: 10392 AN: 10616

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.967 AC: 65804 AN: 68038

Other (OTH) AF: 0.973 AC: 2056 AN: 2114

Alfa AF: 0.966 Hom.: 29193

Bravo AF: 0.972

Asia WGS AF: 0.928 AC: 3230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.30
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs1520832; hg19: chr12-43253415;