chr12-58819362-A-G

Position:

• chr12-58819362-A-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 0.429 in 152,110 control chromosomes in the GnomAD database, including 14,098 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 0.43 (14098 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

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 (AMR) allele frequency at 95% confidence interval = 0.482 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: 0.429 AC: 65241 AN: 151992 Hom.: 14084 Cov.: 33

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.429 AC: 65287 AN: 152110 Hom.: 14098 Cov.: 33 AF XY: 0.431 AC XY: 32041 AN XY: 74348

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.422

Alfa AF: 0.427 Hom.: 2282

Bravo AF: 0.434

Asia WGS AF: 0.452 AC: 1569 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	0.37
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6581219; hg19: chr12-59213144;