12-58407244-C-T

Position:

• chr12-58407244-C-T

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 0.445 in 151,564 control chromosomes in the GnomAD database, including 15,179 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 0.45 (15179 hom., cov: 30)
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.497 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: 0.445 AC: 67460 AN: 151448 Hom.: 15170 Cov.: 30

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.445 AC: 67492 AN: 151564 Hom.: 15179 Cov.: 30 AF XY: 0.447 AC XY: 33082 AN XY: 74036

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.430

Alfa AF: 0.435 Hom.: 33479

Bravo AF: 0.434

Asia WGS AF: 0.481 AC: 1677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3842936; hg19: chr12-58801027;