rs784240

chr18-55766891-T-C

Variant summary

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

The ENST00000654829.1(ENSG00000267284):n.157-18008T>C 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 0.1 in 152,262 control chromosomes in the GnomAD database, including 1,358 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 0.10 (1358 hom., cov: 32)
• Consequence: ENST00000654829.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227

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 = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372130	XR_007066382.1	n.329-18008T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654829.1	n.157-18008T>C		intron_variant, non_coding_transcript_variant
	ENST00000587346.1	n.454+4293T>C		intron_variant, non_coding_transcript_variant		4
	ENST00000589662.1	n.218-18008T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15270 AN: 152146 Hom.: 1357 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0427

Gnomad ASJ AF: 0.0236

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.0518

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0412

Gnomad OTH AF: 0.0784

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

GnomAD4 genome AF: 0.100 AC: 15284 AN: 152262 Hom.: 1358 Cov.: 32 AF XY: 0.102 AC XY: 7558 AN XY: 74442

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.0426

Gnomad4 ASJ AF: 0.0236

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.0518

Gnomad4 NFE AF: 0.0412

Gnomad4 OTH AF: 0.0790

Alfa AF: 0.0547 Hom.: 845

Bravo AF: 0.103

Asia WGS AF: 0.229 AC: 798 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	1.7
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs784240; hg19: chr18-53434122;