12-42596843-A-G

Variant names:

• chr12-42596843-A-G
• rs12370911

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 0.142 in 152,190 control chromosomes in the GnomAD database, including 1,796 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 0.14 (1796 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.178 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: 0.141 AC: 21515 AN: 152072 Hom.: 1789 Cov.: 33

Gnomad AFR AF: 0.0808

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.0918

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.142 AC: 21543 AN: 152190 Hom.: 1796 Cov.: 33 AF XY: 0.140 AC XY: 10435 AN XY: 74406

Gnomad4 AFR AF: 0.0813

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.0922

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.154

Alfa AF: 0.172 Hom.: 4760

Bravo AF: 0.137

Asia WGS AF: 0.108 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.52
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: rs12370911; hg19: chr12-42990645;