18-64251071-G-T

Variant names:

• chr18-64251071-G-T
• rs4514783
• ENST00000588074.1:n.443+7147C>A

Variant summary

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

The ENST00000588074.1(LINC01538):​n.443+7147C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,706 control chromosomes in the GnomAD database, including 24,476 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 0.57 (24476 hom., cov: 31)
• Consequence: LINC01538 ENST00000588074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 1 publications found

Genes affected

LINC01538 (HGNC:51306): (long intergenic non-protein coding RNA 1538)

LINC01924 (HGNC:27600): (long intergenic non-protein coding RNA 1924)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01924	NR_033881.1	n.293+1678G>T		intron_variant	Intron 3 of 9
LINC01538	NR_033983.1	n.443+7147C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01538	ENST00000588074.1	n.443+7147C>A		intron_variant	Intron 2 of 2	1
LINC01924	ENST00000589376.1	n.293+1678G>T		intron_variant	Intron 3 of 9	1
LINC01538	ENST00000649058.1	n.382+7147C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85717 AN: 151590 Hom.: 24461 Cov.: 31

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.565 AC: 85768 AN: 151706 Hom.: 24476 Cov.: 31 AF XY: 0.561 AC XY: 41580 AN XY: 74104

African (AFR) AF: 0.652 AC: 27001 AN: 41400

American (AMR) AF: 0.539 AC: 8225 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1877 AN: 3470

East Asian (EAS) AF: 0.574 AC: 2955 AN: 5150

South Asian (SAS) AF: 0.564 AC: 2716 AN: 4816

European-Finnish (FIN) AF: 0.438 AC: 4567 AN: 10434

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36608 AN: 67866

Other (OTH) AF: 0.558 AC: 1178 AN: 2112

Alfa AF: 0.419 Hom.: 1147

Bravo AF: 0.576

Asia WGS AF: 0.544 AC: 1881 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.8
DANN	Benign	0.44
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4514783; hg19: chr18-61918306;