chr18-24977200-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ENSG00000266573 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01894	NR_146903.1	n.623+10157A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01894	ENST00000665916.1	n.328A>G		splice_region_variant, non_coding_transcript_exon_variant	Exon 2 of 4
LINC01894	ENST00000580984.1	n.326+10157A>G		intron_variant	Intron 1 of 1	2
LINC01894	ENST00000582697.1	n.309+10157A>G		intron_variant	Intron 1 of 1	3

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

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.723

Alfa AF: 0.725 Hom.: 51479

Bravo AF: 0.727

Asia WGS AF: 0.759 AC: 2639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1539829; hg19: chr18-22557164;