chr4-52809667-G-A

Variant names:

• chr4-52809667-G-A
• rs1384847
• ENST00000514957.1:n.416-5486G>A

Variant summary

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

The ENST00000514957.1(LINC01618):​n.416-5486G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0716 in 152,198 control chromosomes in the GnomAD database, including 472 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 0.072 (472 hom., cov: 32)
• Consequence: LINC01618 ENST00000514957.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 3 publications found

Genes affected

LINC01618 (HGNC:):

LINC01618 (HGNC:27195): (long intergenic non-protein coding RNA 1618)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0958 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514957.1. 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
	LINC01618	NR_040106.1		n.416-5486G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01618	ENST00000514957.1	TSL:1	n.416-5486G>A		intron	N/A
	ENSG00000293643	ENST00000650700.1		n.885-6784G>A		intron	N/A
	ENSG00000293643	ENST00000652441.1		n.503+30417G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0717 AC: 10898 AN: 152078 Hom.: 473 Cov.: 32

Gnomad AFR AF: 0.0497

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0307

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0857

Gnomad OTH AF: 0.0526

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

GnomAD4 genome AF: 0.0716 AC: 10892 AN: 152198 Hom.: 472 Cov.: 32 AF XY: 0.0733 AC XY: 5452 AN XY: 74384

African (AFR) AF: 0.0496 AC: 2059 AN: 41542

American (AMR) AF: 0.0306 AC: 468 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0778 AC: 270 AN: 3470

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5190

South Asian (SAS) AF: 0.103 AC: 498 AN: 4820

European-Finnish (FIN) AF: 0.152 AC: 1604 AN: 10570

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0857 AC: 5829 AN: 67996

Other (OTH) AF: 0.0525 AC: 111 AN: 2114

Alfa AF: 0.0769 Hom.: 823

Bravo AF: 0.0589

Asia WGS AF: 0.0580 AC: 203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.2
DANN	Benign	0.75
PhyloP100		-0.54
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1384847; hg19: chr4-53675834;