18-39828717-T-G

Variant names:

• chr18-39828717-T-G
• rs1513691
• ENST00000659647.2:n.342+21152T>G

Variant summary

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

The ENST00000659647.2(LINC01902):​n.342+21152T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 151,770 control chromosomes in the GnomAD database, including 38,775 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 0.71 (38775 hom., cov: 30)
• Consequence: LINC01902 ENST00000659647.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609
• Publications: 3 publications found

Genes affected

LINC01902 (HGNC:52721): (long intergenic non-protein coding RNA 1902)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01902	ENST00000659647.2	n.342+21152T>G		intron_variant	Intron 1 of 7
LINC01902	ENST00000793336.1	n.286+21152T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107743 AN: 151654 Hom.: 38733 Cov.: 30

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.711 AC: 107833 AN: 151770 Hom.: 38775 Cov.: 30 AF XY: 0.714 AC XY: 52954 AN XY: 74172

African (AFR) AF: 0.623 AC: 25801 AN: 41388

American (AMR) AF: 0.592 AC: 9016 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2451 AN: 3466

East Asian (EAS) AF: 0.766 AC: 3919 AN: 5118

South Asian (SAS) AF: 0.794 AC: 3817 AN: 4806

European-Finnish (FIN) AF: 0.792 AC: 8376 AN: 10572

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52149 AN: 67888

Other (OTH) AF: 0.707 AC: 1491 AN: 2108

Alfa AF: 0.684 Hom.: 2199

Bravo AF: 0.687

Asia WGS AF: 0.771 AC: 2686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.82
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs1513691; hg19: chr18-37408681;