12-42859612-T-G

Variant names:

• chr12-42859612-T-G
• rs1520832

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.991

Gnomad4 AMR AF: 0.971

Gnomad4 ASJ AF: 0.951

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.958

Gnomad4 FIN AF: 0.979

Gnomad4 NFE AF: 0.967

Gnomad4 OTH AF: 0.973

Alfa AF: 0.953 Hom.: 12193

Bravo AF: 0.972

Asia WGS AF: 0.928 AC: 3230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1520832; hg19: chr12-43253415;