12-76638849-T-C

Variant names:

• chr12-76638849-T-C
• rs2632214
• ENST00000832799.1:n.554+5793T>C

Variant summary

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

The ENST00000832799.1(ENSG00000257526):​n.554+5793T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,230 control chromosomes in the GnomAD database, including 2,556 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 0.15 (2556 hom., cov: 32)
• Consequence: ENSG00000257526 ENST00000832799.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 7 publications found

Genes affected

ENSG00000257526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832799.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257526	ENST00000832799.1		n.554+5793T>C		intron	N/A
	ENSG00000257526	ENST00000832800.1		n.564+5793T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23521 AN: 152112 Hom.: 2545 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.155 AC: 23566 AN: 152230 Hom.: 2556 Cov.: 32 AF XY: 0.162 AC XY: 12033 AN XY: 74430

African (AFR) AF: 0.146 AC: 6060 AN: 41550

American (AMR) AF: 0.129 AC: 1976 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 496 AN: 3470

East Asian (EAS) AF: 0.636 AC: 3291 AN: 5178

South Asian (SAS) AF: 0.222 AC: 1072 AN: 4824

European-Finnish (FIN) AF: 0.197 AC: 2083 AN: 10588

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8179 AN: 68010

Other (OTH) AF: 0.154 AC: 325 AN: 2116

Alfa AF: 0.124 Hom.: 2149

Bravo AF: 0.149

Asia WGS AF: 0.391 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.31
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2632214; hg19: chr12-77032629;