12-42859612-T-G

Position:

• chr12-42859612-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;