18-24977200-T-C

Variant names:

• chr18-24977200-T-C
• rs1539829
• ENST00000665916.1:n.328A>G

Variant summary

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

The ENST00000665916.1(LINC01894):​n.328A>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 152,094 control chromosomes in the GnomAD database, including 40,226 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 0.73 (40226 hom., cov: 32)
• Consequence: LINC01894 ENST00000665916.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 1 publications found

Genes affected

LINC01894 (HGNC:52713): (long intergenic non-protein coding RNA 1894)

ENSG00000266573 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665916.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01894	NR_146903.1		n.623+10157A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01894	ENST00000665916.1		n.328A>G		splice_region non_coding_transcript_exon	Exon 2 of 4
	LINC01894	ENST00000781984.1		n.381A>G		splice_region non_coding_transcript_exon	Exon 2 of 3
	LINC01894	ENST00000580984.1	TSL:2	n.326+10157A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110563 AN: 151976 Hom.: 40187 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.728 AC: 110657 AN: 152094 Hom.: 40226 Cov.: 32 AF XY: 0.728 AC XY: 54092 AN XY: 74334

African (AFR) AF: 0.727 AC: 30191 AN: 41506

American (AMR) AF: 0.737 AC: 11276 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2484 AN: 3468

East Asian (EAS) AF: 0.780 AC: 4018 AN: 5148

South Asian (SAS) AF: 0.780 AC: 3760 AN: 4820

European-Finnish (FIN) AF: 0.705 AC: 7457 AN: 10570

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.722 AC: 49088 AN: 67974

Other (OTH) AF: 0.723 AC: 1526 AN: 2112

Alfa AF: 0.722 Hom.: 117304

Bravo AF: 0.727

Asia WGS AF: 0.759 AC: 2639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.37
DANN	Benign	0.51
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1539829; hg19: chr18-22557164;