18-71542251-G-T

Variant names:

• chr18-71542251-G-T
• rs2096952
• ENST00000568095.5:n.248+6348C>A

Variant summary

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

The ENST00000568095.5(LINC01541):​n.248+6348C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,004 control chromosomes in the GnomAD database, including 2,592 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 0.17 (2592 hom., cov: 31)
• Consequence: LINC01541 ENST00000568095.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 0 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) 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
LINC01541	NR_038325.1	n.248+6348C>A		intron_variant	Intron 2 of 6
LINC01541	NR_038326.1	n.248+6348C>A		intron_variant	Intron 2 of 4
LOC107985179	XR_001753502.1	n.65-5720G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01541	ENST00000568095.5	n.248+6348C>A		intron_variant	Intron 2 of 6	1
LINC01541	ENST00000566582.1	n.229+6348C>A		intron_variant	Intron 2 of 4	2
ENSG00000298599	ENST00000756734.1	n.97-5720G>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25061 AN: 151886 Hom.: 2589 Cov.: 31

Gnomad AFR AF: 0.0583

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.165 AC: 25081 AN: 152004 Hom.: 2592 Cov.: 31 AF XY: 0.172 AC XY: 12751 AN XY: 74286

African (AFR) AF: 0.0583 AC: 2417 AN: 41484

American (AMR) AF: 0.141 AC: 2154 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 787 AN: 3468

East Asian (EAS) AF: 0.222 AC: 1144 AN: 5162

South Asian (SAS) AF: 0.343 AC: 1648 AN: 4808

European-Finnish (FIN) AF: 0.262 AC: 2762 AN: 10552

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.200 AC: 13589 AN: 67960

Other (OTH) AF: 0.164 AC: 347 AN: 2112

Alfa AF: 0.108 Hom.: 183

Bravo AF: 0.144

Asia WGS AF: 0.274 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.39
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2096952; hg19: chr18-69209487;