18-71533616-C-T

Variant names:

• chr18-71533616-C-T
• rs7227159
• ENST00000568095.5:n.331+598G>A

Variant summary

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

The ENST00000568095.5(LINC01541):​n.331+598G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 151,066 control chromosomes in the GnomAD database, including 3,209 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 0.20 (3209 hom., cov: 32)
• Consequence: LINC01541 ENST00000568095.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 1 publications found

Genes affected

LINC01541 (HGNC:51309): (long intergenic non-protein coding RNA 1541)

ENSG00000298599 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01541	NR_038325.1	n.331+598G>A		intron_variant	Intron 3 of 6
LINC01541	NR_038326.1	n.331+598G>A		intron_variant	Intron 3 of 4
LOC107985179	XR_001753502.1	n.65-14355C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01541	ENST00000568095.5	n.331+598G>A		intron_variant	Intron 3 of 6	1
LINC01541	ENST00000566582.1	n.312+598G>A		intron_variant	Intron 3 of 4	2
ENSG00000298599	ENST00000756734.1	n.97-14355C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30500 AN: 150948 Hom.: 3201 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.202 AC: 30555 AN: 151066 Hom.: 3209 Cov.: 32 AF XY: 0.200 AC XY: 14738 AN XY: 73776

African (AFR) AF: 0.252 AC: 10382 AN: 41276

American (AMR) AF: 0.180 AC: 2721 AN: 15094

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 642 AN: 3468

East Asian (EAS) AF: 0.155 AC: 793 AN: 5130

South Asian (SAS) AF: 0.112 AC: 538 AN: 4804

European-Finnish (FIN) AF: 0.174 AC: 1819 AN: 10470

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.193 AC: 13009 AN: 67526

Other (OTH) AF: 0.202 AC: 424 AN: 2098

Alfa AF: 0.193 Hom.: 1711

Bravo AF: 0.206

Asia WGS AF: 0.159 AC: 551 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.80
DANN	Benign	0.31
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7227159; hg19: chr18-69200852;