ENST00000568095.5:n.248+6705A>G

Variant names:

• chr18-71541894-T-C
• rs719328
• ENST00000568095.5:n.248+6705A>G

Variant summary

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

The ENST00000568095.5(LINC01541):​n.248+6705A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,162 control chromosomes in the GnomAD database, including 1,911 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 0.14 (1911 hom., cov: 32)
• Consequence: LINC01541 ENST00000568095.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• 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 (NFE) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01541	NR_038325.1	n.248+6705A>G		intron_variant	Intron 2 of 6
LINC01541	NR_038326.1	n.248+6705A>G		intron_variant	Intron 2 of 4
LOC107985179	XR_001753502.1	n.65-6077T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01541	ENST00000568095.5	n.248+6705A>G		intron_variant	Intron 2 of 6	1
LINC01541	ENST00000566582.1	n.229+6705A>G		intron_variant	Intron 2 of 4	2
ENSG00000298599	ENST00000756734.1	n.97-6077T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22015 AN: 152044 Hom.: 1909 Cov.: 32

Gnomad AFR AF: 0.0503

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.145 AC: 22033 AN: 152162 Hom.: 1911 Cov.: 32 AF XY: 0.144 AC XY: 10747 AN XY: 74396

African (AFR) AF: 0.0503 AC: 2089 AN: 41546

American (AMR) AF: 0.161 AC: 2453 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3470

East Asian (EAS) AF: 0.155 AC: 797 AN: 5152

South Asian (SAS) AF: 0.123 AC: 592 AN: 4828

European-Finnish (FIN) AF: 0.174 AC: 1844 AN: 10596

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13060 AN: 67974

Other (OTH) AF: 0.158 AC: 334 AN: 2116

Alfa AF: 0.178 Hom.: 1289

Bravo AF: 0.141

Asia WGS AF: 0.147 AC: 511 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	4.4
DANN	Benign	0.31
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs719328; hg19: chr18-69209130;