18-51492510-C-T

Variant names:

• chr18-51492510-C-T
• rs1369766
• ENST00000435144.7:n.220-68083C>T

Variant summary

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

The ENST00000580841.1(LINC01630):​n.217-68083C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 151,980 control chromosomes in the GnomAD database, including 21,027 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 0.50 (21027 hom., cov: 32)
• Consequence: LINC01630 ENST00000580841.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.598

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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01630	NR_040074.1	n.217-68083C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01630	ENST00000435144.7	n.220-68083C>T		intron_variant	Intron 1 of 6	5
LINC01630	ENST00000580841.1	n.217-68083C>T		intron_variant	Intron 1 of 2	4
LINC01630	ENST00000582689.5	n.328-32452C>T		intron_variant	Intron 3 of 5	4

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75619 AN: 151862 Hom.: 21024 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.498 AC: 75642 AN: 151980 Hom.: 21027 Cov.: 32 AF XY: 0.500 AC XY: 37173 AN XY: 74304

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.518

Alfa AF: 0.583 Hom.: 36317

Bravo AF: 0.477

Asia WGS AF: 0.508 AC: 1767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.68
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1369766; hg19: chr18-49018880;