18-51582627-A-G

Variant names:

• chr18-51582627-A-G
• rs728683
• ENST00000660545.1:n.1294A>G

Variant summary

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

The ENST00000660545.1(LINC01630):​n.1294A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,168 control chromosomes in the GnomAD database, including 42,486 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 0.74 (42486 hom., cov: 33)
• Consequence: LINC01630 ENST00000660545.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592
• Publications: 8 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660545.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01630	ENST00000660545.1		n.1294A>G		non_coding_transcript_exon	Exon 6 of 6
	LINC01630	ENST00000435144.7	TSL:5	n.4200+189A>G		intron	N/A
	LINC01630	ENST00000635103.1	TSL:5	n.551+189A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112420 AN: 152050 Hom.: 42465 Cov.: 33

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.739 AC: 112484 AN: 152168 Hom.: 42486 Cov.: 33 AF XY: 0.747 AC XY: 55586 AN XY: 74398

African (AFR) AF: 0.584 AC: 24218 AN: 41470

American (AMR) AF: 0.828 AC: 12675 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2325 AN: 3472

East Asian (EAS) AF: 0.930 AC: 4819 AN: 5180

South Asian (SAS) AF: 0.806 AC: 3885 AN: 4820

European-Finnish (FIN) AF: 0.873 AC: 9253 AN: 10602

Middle Eastern (MID) AF: 0.747 AC: 218 AN: 292

European-Non Finnish (NFE) AF: 0.777 AC: 52836 AN: 68006

Other (OTH) AF: 0.740 AC: 1565 AN: 2114

Alfa AF: 0.759 Hom.: 52045

Bravo AF: 0.731

Asia WGS AF: 0.855 AC: 2972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.72
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs728683; hg19: chr18-49108997;