rs12326693

Variant names:

• chr18-55768238-C-T
• rs12326693
• ENST00000587346.1:n.455-4469C>T

Variant summary

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

The ENST00000587346.1(ENSG00000267284):​n.455-4469C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,070 control chromosomes in the GnomAD database, including 4,407 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 0.23 (4407 hom., cov: 32)
• Consequence: ENSG00000267284 ENST00000587346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 2 publications found

Genes affected

ENSG00000267284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372130	XR_007066382.1	n.329-16661C>T		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267284	ENST00000587346.1	n.455-4469C>T		intron_variant	Intron 3 of 4	4
ENSG00000267284	ENST00000589662.1	n.218-16661C>T		intron_variant	Intron 1 of 3	5
ENSG00000267284	ENST00000654829.1	n.157-16661C>T		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34641 AN: 151952 Hom.: 4400 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.228 AC: 34684 AN: 152070 Hom.: 4407 Cov.: 32 AF XY: 0.230 AC XY: 17081 AN XY: 74326

African (AFR) AF: 0.126 AC: 5239 AN: 41498

American (AMR) AF: 0.342 AC: 5219 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3466

East Asian (EAS) AF: 0.145 AC: 753 AN: 5184

South Asian (SAS) AF: 0.162 AC: 784 AN: 4826

European-Finnish (FIN) AF: 0.261 AC: 2753 AN: 10558

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18518 AN: 67952

Other (OTH) AF: 0.225 AC: 473 AN: 2104

Alfa AF: 0.250 Hom.: 858

Bravo AF: 0.230

Asia WGS AF: 0.200 AC: 696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.27
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs12326693; hg19: chr18-53435469;