chr18-10408495-C-T

Variant names:

• chr18-10408495-C-T
• rs7228576
• ENST00000567609.1:n.1591-2280G>A

Variant summary

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

The ENST00000567609.1(LINC01254):​n.1591-2280G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,050 control chromosomes in the GnomAD database, including 3,246 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 0.18 (3246 hom., cov: 32)
• Consequence: LINC01254 ENST00000567609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01254	NR_110775.1	n.1591-2280G>A		intron_variant	Intron 1 of 2
LOC105371988	XR_935142.4	n.737+1551C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01254	ENST00000567609.1	n.1591-2280G>A		intron_variant	Intron 1 of 2	1
ENSG00000287563	ENST00000671418.1	n.387+1551C>T		intron_variant	Intron 1 of 1
ENSG00000287563	ENST00000754460.1	n.514-13002C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27745 AN: 151932 Hom.: 3246 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0120

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.0660

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.183 AC: 27773 AN: 152050 Hom.: 3246 Cov.: 32 AF XY: 0.177 AC XY: 13158 AN XY: 74328

African (AFR) AF: 0.334 AC: 13829 AN: 41438

American (AMR) AF: 0.121 AC: 1851 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 598 AN: 3468

East Asian (EAS) AF: 0.0120 AC: 62 AN: 5168

South Asian (SAS) AF: 0.169 AC: 811 AN: 4812

European-Finnish (FIN) AF: 0.0660 AC: 699 AN: 10592

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9389 AN: 67972

Other (OTH) AF: 0.177 AC: 373 AN: 2112

Alfa AF: 0.153 Hom.: 6909

Bravo AF: 0.191

Asia WGS AF: 0.107 AC: 376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.58
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7228576; hg19: chr18-10408492;