ENST00000518556.5:n.224-203A>G

Variant names:

• chr8-57202716-A-G
• rs6982990
• ENST00000518556.5:n.224-203A>G

Variant summary

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

The ENST00000518556.5(LINC01606):​n.224-203A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 151,792 control chromosomes in the GnomAD database, including 2,669 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 0.17 (2669 hom., cov: 32)
• Consequence: LINC01606 ENST00000518556.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 2 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=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01606	ENST00000518556.5	TSL:3	n.224-203A>G		intron	N/A
	LINC01606	ENST00000519241.6	TSL:3	n.558+8705A>G		intron	N/A
	LINC01606	ENST00000521653.6	TSL:4	n.228-5293A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26420 AN: 151672 Hom.: 2650 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0803

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.174 AC: 26477 AN: 151792 Hom.: 2669 Cov.: 32 AF XY: 0.173 AC XY: 12844 AN XY: 74158

African (AFR) AF: 0.286 AC: 11835 AN: 41374

American (AMR) AF: 0.129 AC: 1971 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3468

East Asian (EAS) AF: 0.138 AC: 707 AN: 5116

South Asian (SAS) AF: 0.0802 AC: 385 AN: 4800

European-Finnish (FIN) AF: 0.168 AC: 1771 AN: 10528

Middle Eastern (MID) AF: 0.132 AC: 38 AN: 288

European-Non Finnish (NFE) AF: 0.133 AC: 9020 AN: 67956

Other (OTH) AF: 0.161 AC: 339 AN: 2104

Alfa AF: 0.161 Hom.: 273

Bravo AF: 0.177

Asia WGS AF: 0.120 AC: 416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.7
DANN	Benign	0.13
PhyloP100		-1.7
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: rs6982990; hg19: chr8-58115275;