18-55758439-C-T

Position:

• chr18-55758439-C-T

Variant summary

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

The ENST00000654829.1(ENSG00000267284):​n.157-26460C>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 0.757 in 151,994 control chromosomes in the GnomAD database, including 43,782 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 0.76 (43782 hom., cov: 31)
• Consequence: ENST00000654829.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372130	XR_007066382.1	n.329-26460C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654829.1	n.157-26460C>T		intron_variant, non_coding_transcript_variant
	ENST00000587346.1	n.140-2864C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000589662.1	n.218-26460C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000592936.1	n.473-601C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.757 AC: 114927 AN: 151878 Hom.: 43758 Cov.: 31

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.757 AC: 114997 AN: 151994 Hom.: 43782 Cov.: 31 AF XY: 0.758 AC XY: 56341 AN XY: 74292

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.815

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.795

Alfa AF: 0.775 Hom.: 5363

Bravo AF: 0.763

Asia WGS AF: 0.678 AC: 2354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.22
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3745044; hg19: chr18-53425670;