18-55738151-C-T

Position:

• chr18-55738151-C-T

Variant summary

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

The ENST00000654829.1(ENSG00000267284):​n.157-46748C>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 0.497 in 151,404 control chromosomes in the GnomAD database, including 19,258 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 0.50 (19258 hom., cov: 29)
• Consequence: ENST00000654829.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372130	XR_007066382.1	n.329-46748C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654829.1	n.157-46748C>T		intron_variant, non_coding_transcript_variant
	ENST00000587346.1	n.139+16617C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000589662.1	n.217+16617C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000592936.1	n.472+16617C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75209 AN: 151286 Hom.: 19241 Cov.: 29

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.497 AC: 75271 AN: 151404 Hom.: 19258 Cov.: 29 AF XY: 0.502 AC XY: 37099 AN XY: 73930

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.504

Alfa AF: 0.490 Hom.: 37429

Bravo AF: 0.490

Asia WGS AF: 0.705 AC: 2453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs784254; hg19: chr18-53405382;