18-51425959-T-C

Variant names:

• chr18-51425959-T-C
• rs321879
• ENST00000435144.7:n.219+33702T>C

Variant summary

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

The ENST00000578152.5(LINC01630):​n.216+33702T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 152,060 control chromosomes in the GnomAD database, including 20,442 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 0.49 (20442 hom., cov: 33)
• Consequence: LINC01630 ENST00000578152.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000578152.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01630	NR_040074.1		n.216+33702T>C		intron	N/A
	LINC01630	NR_040075.1		n.216+33702T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01630	ENST00000435144.7	TSL:5	n.219+33702T>C		intron	N/A
	LINC01630	ENST00000578152.5	TSL:2	n.216+33702T>C		intron	N/A
	LINC01630	ENST00000580841.1	TSL:4	n.216+33702T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74711 AN: 151940 Hom.: 20428 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.492 AC: 74748 AN: 152060 Hom.: 20442 Cov.: 33 AF XY: 0.499 AC XY: 37100 AN XY: 74324

African (AFR) AF: 0.241 AC: 10002 AN: 41510

American (AMR) AF: 0.620 AC: 9467 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1968 AN: 3466

East Asian (EAS) AF: 0.752 AC: 3886 AN: 5170

South Asian (SAS) AF: 0.675 AC: 3253 AN: 4818

European-Finnish (FIN) AF: 0.554 AC: 5846 AN: 10550

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38562 AN: 67964

Other (OTH) AF: 0.488 AC: 1026 AN: 2104

Alfa AF: 0.507 Hom.: 2693

Bravo AF: 0.484

Asia WGS AF: 0.643 AC: 2232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.65
PhyloP100		0.083

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs321879;

hg19: chr18-48952329;