18-51352352-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000582689.5(LINC01630):n.130+5974A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01630	ENST00000582689.5	n.130+5974A>G		intron_variant, non_coding_transcript_variant		4
LINC01630	ENST00000635503.2	n.130+5974A>G		intron_variant, non_coding_transcript_variant		5
LINC01630	ENST00000662191.1	n.104+5974A>G		intron_variant, non_coding_transcript_variant
LINC01630	ENST00000666962.1	n.65+5974A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.840

Gnomad4 NFE AF: 0.899

Gnomad4 OTH AF: 0.775

Alfa AF: 0.842 Hom.: 13211

Bravo AF: 0.760

Asia WGS AF: 0.711 AC: 2472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.2
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1463389; hg19: chr18-48878722;