18-55733603-C-T

Position:

• chr18-55733603-C-T

Variant summary

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

The ENST00000654829.1(ENSG00000267284):​n.157-51296C>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 0.0778 in 151,958 control chromosomes in the GnomAD database, including 895 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 0.078 (895 hom., cov: 32)
• Consequence: ENST00000654829.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130

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 (EAS) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372130	XR_007066382.1	n.329-51296C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654829.1	n.157-51296C>T		intron_variant, non_coding_transcript_variant
	ENST00000587346.1	n.139+12069C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000589662.1	n.217+12069C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000592936.1	n.472+12069C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0779 AC: 11830 AN: 151840 Hom.: 897 Cov.: 32

Gnomad AFR AF: 0.0150

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0562

Gnomad ASJ AF: 0.0993

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0844

Gnomad OTH AF: 0.0849

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

GnomAD4 genome AF: 0.0778 AC: 11825 AN: 151958 Hom.: 895 Cov.: 32 AF XY: 0.0807 AC XY: 5988 AN XY: 74246

Gnomad4 AFR AF: 0.0150

Gnomad4 AMR AF: 0.0560

Gnomad4 ASJ AF: 0.0993

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.0975

Gnomad4 NFE AF: 0.0845

Gnomad4 OTH AF: 0.0844

Alfa AF: 0.0763 Hom.: 294

Bravo AF: 0.0729

Asia WGS AF: 0.245 AC: 853 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	3.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17089925; hg19: chr18-53400834;