rs12326693

chr18-55768238-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654829.1(ENSG00000267284):n.157-16661C>T variant causes a intron, non coding transcript 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: ENST00000654829.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105372130	XR_007066382.1	n.329-16661C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654829.1	n.157-16661C>T		intron_variant, non_coding_transcript_variant
	ENST00000587346.1	n.455-4469C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000589662.1	n.218-16661C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.225

Alfa AF: 0.254 Hom.: 850

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12326693; hg19: chr18-53435469;