rs784233

chr18-55757015-C-T

Variant summary

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

The ENST00000654829.1(ENSG00000267284):n.157-27884C>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 0.083 in 152,050 control chromosomes in the GnomAD database, including 908 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 0.083 (908 hom., cov: 29)
• Consequence: ENST00000654829.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372130	XR_007066382.1	n.329-27884C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654829.1	n.157-27884C>T		intron_variant, non_coding_transcript_variant
	ENST00000587346.1	n.140-4288C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000589662.1	n.218-27884C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000592936.1	n.473-2025C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0829 AC: 12593 AN: 151932 Hom.: 909 Cov.: 29

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0350

Gnomad ASJ AF: 0.0236

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0528

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0412

Gnomad OTH AF: 0.0662

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

GnomAD4 genome AF: 0.0830 AC: 12613 AN: 152050 Hom.: 908 Cov.: 29 AF XY: 0.0845 AC XY: 6282 AN XY: 74314

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0350

Gnomad4 ASJ AF: 0.0236

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.0528

Gnomad4 NFE AF: 0.0412

Gnomad4 OTH AF: 0.0664

Alfa AF: 0.0463 Hom.: 154

Bravo AF: 0.0830

Asia WGS AF: 0.226 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.8
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs784233; hg19: chr18-53424246;