12-57668884-C-T

Variant names:

• chr12-57668884-C-T
• rs10876993

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 0.57 in 150,950 control chromosomes in the GnomAD database, including 25,522 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 (25522 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 33 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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: 0.570 AC: 85971 AN: 150838 Hom.: 25520 Cov.: 27

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.570 AC: 86003 AN: 150950 Hom.: 25522 Cov.: 27 AF XY: 0.563 AC XY: 41467 AN XY: 73668

African (AFR) AF: 0.424 AC: 17416 AN: 41078

American (AMR) AF: 0.627 AC: 9493 AN: 15132

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2359 AN: 3468

East Asian (EAS) AF: 0.358 AC: 1828 AN: 5110

South Asian (SAS) AF: 0.383 AC: 1833 AN: 4790

European-Finnish (FIN) AF: 0.592 AC: 6079 AN: 10266

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

European-Non Finnish (NFE) AF: 0.664 AC: 45035 AN: 67814

Other (OTH) AF: 0.625 AC: 1307 AN: 2092

Alfa AF: 0.624 Hom.: 59784

Bravo AF: 0.568

Asia WGS AF: 0.383 AC: 1335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.52
PhyloP100		0.19
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10876993; hg19: chr12-58062667;