ENST00000588074.1:n.444-9127G>C

Variant names:

• chr18-64224173-C-G
• rs11876820
• ENST00000588074.1:n.444-9127G>C

Variant summary

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

The ENST00000588074.1(LINC01538):​n.444-9127G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 152,046 control chromosomes in the GnomAD database, including 34,074 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 0.65 (34074 hom., cov: 32)
• Consequence: LINC01538 ENST00000588074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01924	NR_033881.1	n.201-25128C>G		intron_variant	Intron 2 of 9
LINC01538	NR_033983.1	n.444-9127G>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01538	ENST00000588074.1	n.444-9127G>C		intron_variant	Intron 2 of 2	1
LINC01924	ENST00000589376.1	n.201-25128C>G		intron_variant	Intron 2 of 9	1
LINC01538	ENST00000649058.1	n.383-31351G>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98638 AN: 151928 Hom.: 34025 Cov.: 32

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.649 AC: 98742 AN: 152046 Hom.: 34074 Cov.: 32 AF XY: 0.647 AC XY: 48054 AN XY: 74308

African (AFR) AF: 0.902 AC: 37472 AN: 41522

American (AMR) AF: 0.601 AC: 9172 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1857 AN: 3462

East Asian (EAS) AF: 0.709 AC: 3659 AN: 5158

South Asian (SAS) AF: 0.584 AC: 2809 AN: 4814

European-Finnish (FIN) AF: 0.509 AC: 5365 AN: 10540

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36451 AN: 67976

Other (OTH) AF: 0.626 AC: 1320 AN: 2108

Alfa AF: 0.418 Hom.: 999

Bravo AF: 0.668

Asia WGS AF: 0.657 AC: 2283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.58
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs11876820; hg19: chr18-61891408;