rs12826786

Variant names:

• chr12-53961717-C-T
• rs12826786
• ENST00000717831.1:n.260+2286G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000717831.1(ENSG00000293680):​n.260+2286G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,038 control chromosomes in the GnomAD database, including 11,144 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 0.37 (11144 hom., cov: 32)
• Consequence: ENSG00000293680 ENST00000717831.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 99 publications found

Genes affected

ENSG00000293680 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 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
ENSG00000293680	ENST00000717831.1	n.260+2286G>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56906 AN: 151920 Hom.: 11104 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.375 AC: 57004 AN: 152038 Hom.: 11144 Cov.: 32 AF XY: 0.368 AC XY: 27378 AN XY: 74318

African (AFR) AF: 0.487 AC: 20187 AN: 41462

American (AMR) AF: 0.377 AC: 5756 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1570 AN: 3470

East Asian (EAS) AF: 0.206 AC: 1064 AN: 5176

South Asian (SAS) AF: 0.353 AC: 1699 AN: 4808

European-Finnish (FIN) AF: 0.241 AC: 2544 AN: 10574

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23038 AN: 67964

Other (OTH) AF: 0.378 AC: 797 AN: 2106

Alfa AF: 0.386 Hom.: 1720

Bravo AF: 0.390

Asia WGS AF: 0.321 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.5
DANN	Benign	0.85
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs12826786; hg19: chr12-54355501;