8-57202184-G-A

Variant names:

• chr8-57202184-G-A
• rs2318144
• ENST00000518556.5:n.224-735G>A

Variant summary

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

The ENST00000518556.5(LINC01606):​n.224-735G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,170 control chromosomes in the GnomAD database, including 994 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 0.11 (994 hom., cov: 32)
• Consequence: LINC01606 ENST00000518556.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 7 publications found

Genes affected

LINC01606 (HGNC:51656): (long intergenic non-protein coding RNA 1606)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518556.5. 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
	LINC01606	ENST00000518556.5	TSL:3	n.224-735G>A		intron	N/A
	LINC01606	ENST00000519241.6	TSL:3	n.558+8173G>A		intron	N/A
	LINC01606	ENST00000521653.6	TSL:4	n.228-5825G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17088 AN: 152052 Hom.: 989 Cov.: 32

Gnomad AFR AF: 0.0797

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0725

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.112 AC: 17110 AN: 152170 Hom.: 994 Cov.: 32 AF XY: 0.112 AC XY: 8353 AN XY: 74396

African (AFR) AF: 0.0800 AC: 3322 AN: 41540

American (AMR) AF: 0.103 AC: 1569 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0971 AC: 337 AN: 3470

East Asian (EAS) AF: 0.137 AC: 707 AN: 5142

South Asian (SAS) AF: 0.0723 AC: 349 AN: 4826

European-Finnish (FIN) AF: 0.166 AC: 1758 AN: 10588

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.129 AC: 8745 AN: 68008

Other (OTH) AF: 0.113 AC: 238 AN: 2112

Alfa AF: 0.126 Hom.: 1256

Bravo AF: 0.109

Asia WGS AF: 0.102 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.35
PhyloP100		0.33
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: rs2318144; hg19: chr8-58114743;