12-42613594-T-C

Position:

• chr12-42613594-T-C

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 0.838 in 152,040 control chromosomes in the GnomAD database, including 55,421 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 0.84 (55421 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127398 AN: 151922 Hom.: 55401 Cov.: 31

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.954

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.950

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.838 AC: 127458 AN: 152040 Hom.: 55421 Cov.: 31 AF XY: 0.841 AC XY: 62494 AN XY: 74306

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.883

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 0.877

Gnomad4 SAS AF: 0.948

Gnomad4 FIN AF: 0.954

Gnomad4 NFE AF: 0.950

Gnomad4 OTH AF: 0.835

Alfa AF: 0.874 Hom.: 6931

Bravo AF: 0.823

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	11
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7964774; hg19: chr12-43007396;