18-10410178-A-G

Variant names:

• chr18-10410178-A-G
• rs182276
• ENST00000567609.1:n.1590+2603T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000567609.1(LINC01254):​n.1590+2603T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.952 in 152,240 control chromosomes in the GnomAD database, including 69,199 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 0.95 (69199 hom., cov: 31)
• Consequence: LINC01254 ENST00000567609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 3 publications found

Genes affected

LINC01254 (HGNC:49870): (long intergenic non-protein coding RNA 1254)

ENSG00000287563 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000567609.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01254	NR_110775.1		n.1590+2603T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01254	ENST00000567609.1	TSL:1	n.1590+2603T>C		intron	N/A
	LINC01254	ENST00000754756.1		n.663T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000287563	ENST00000671418.1		n.387+3234A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.952 AC: 144888 AN: 152122 Hom.: 69148 Cov.: 31

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.973

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.978

Gnomad OTH AF: 0.950

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

GnomAD4 genome AF: 0.952 AC: 144999 AN: 152240 Hom.: 69199 Cov.: 31 AF XY: 0.954 AC XY: 70987 AN XY: 74438

African (AFR) AF: 0.887 AC: 36822 AN: 41508

American (AMR) AF: 0.976 AC: 14939 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.938 AC: 3256 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5166 AN: 5168

South Asian (SAS) AF: 0.973 AC: 4694 AN: 4824

European-Finnish (FIN) AF: 0.985 AC: 10459 AN: 10622

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.978 AC: 66519 AN: 68022

Other (OTH) AF: 0.951 AC: 2010 AN: 2114

Alfa AF: 0.959 Hom.: 10338

Bravo AF: 0.950

Asia WGS AF: 0.981 AC: 3412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.57
DANN	Benign	0.76
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs182276; hg19: chr18-10410175;