18-71542251-G-T

Position:

• chr18-71542251-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC01541 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC01541	NR_038325.1	n.248+6348C>A		intron_variant
LINC01541	NR_038326.1	n.248+6348C>A		intron_variant
LOC107985179	XR_001753502.1	n.65-5720G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01541	ENST00000568095.5	n.248+6348C>A		intron_variant		1
LINC01541	ENST00000566582.1	n.229+6348C>A		intron_variant		2

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

Gnomad4 AFR AF: 0.0583

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.164

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2096952; hg19: chr18-69209487;