chr18-51352352-A-G

Variant names:

• chr18-51352352-A-G
• rs1463389
• ENST00000582689.5:n.130+5974A>G

Variant summary

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

The ENST00000582689.5(LINC01630):​n.130+5974A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 152,162 control chromosomes in the GnomAD database, including 47,470 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 0.78 (47470 hom., cov: 32)
• Consequence: LINC01630 ENST00000582689.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 2 publications found

Genes affected

LINC01630 (HGNC:52295): (long intergenic non-protein coding RNA 1630)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000582689.5. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01630	ENST00000582689.5	TSL:4	n.130+5974A>G		intron	N/A
	LINC01630	ENST00000635503.2	TSL:5	n.130+5974A>G		intron	N/A
	LINC01630	ENST00000662191.2		n.104+5974A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118202 AN: 152044 Hom.: 47457 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.777 AC: 118250 AN: 152162 Hom.: 47470 Cov.: 32 AF XY: 0.774 AC XY: 57555 AN XY: 74406

African (AFR) AF: 0.573 AC: 23771 AN: 41496

American (AMR) AF: 0.754 AC: 11520 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2937 AN: 3472

East Asian (EAS) AF: 0.625 AC: 3228 AN: 5168

South Asian (SAS) AF: 0.845 AC: 4078 AN: 4824

European-Finnish (FIN) AF: 0.840 AC: 8902 AN: 10598

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 61100 AN: 67996

Other (OTH) AF: 0.775 AC: 1639 AN: 2114

Alfa AF: 0.836 Hom.: 13348

Bravo AF: 0.760

Asia WGS AF: 0.711 AC: 2472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.43
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1463389; hg19: chr18-48878722;