12-58356897-T-C

Position:

• chr12-58356897-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 0.328 in 152,080 control chromosomes in the GnomAD database, including 8,364 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 0.33 (8364 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.345 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: 0.328 AC: 49823 AN: 151962 Hom.: 8365 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.328 AC: 49833 AN: 152080 Hom.: 8364 Cov.: 33 AF XY: 0.332 AC XY: 24642 AN XY: 74324

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.320

Alfa AF: 0.333 Hom.: 14792

Bravo AF: 0.308

Asia WGS AF: 0.299 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	13
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1795708; hg19: chr12-58750680;