chr12-57662980-C-T

Position:

• chr12-57662980-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 0.574 in 152,050 control chromosomes in the GnomAD database, including 26,010 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 0.57 (26010 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 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: 0.574 AC: 87245 AN: 151932 Hom.: 26008 Cov.: 33

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.574 AC: 87278 AN: 152050 Hom.: 26010 Cov.: 33 AF XY: 0.567 AC XY: 42154 AN XY: 74300

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.627

Alfa AF: 0.605 Hom.: 8096

Bravo AF: 0.572

Asia WGS AF: 0.385 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.44
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1689595; hg19: chr12-58056763;