12-57662980-C-T

Variant names:

• chr12-57662980-C-T
• rs1689595

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.439 AC: 18210 AN: 41456

American (AMR) AF: 0.630 AC: 9631 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2359 AN: 3470

East Asian (EAS) AF: 0.357 AC: 1845 AN: 5170

South Asian (SAS) AF: 0.382 AC: 1841 AN: 4816

European-Finnish (FIN) AF: 0.593 AC: 6267 AN: 10562

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45148 AN: 67972

Other (OTH) AF: 0.627 AC: 1323 AN: 2110

Alfa AF: 0.612 Hom.: 13133

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
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1689595; hg19: chr12-58056763;