ENST00000518556.5:n.224-3425A>G

Variant names:

• chr8-57199494-A-G
• rs7463453
• ENST00000518556.5:n.224-3425A>G

Variant summary

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

The ENST00000518556.5(LINC01606):​n.224-3425A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 151,986 control chromosomes in the GnomAD database, including 2,620 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 (2620 hom., cov: 33)
• Consequence: LINC01606 ENST00000518556.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 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.224-3425A>G		intron	N/A
	LINC01606	ENST00000519241.6	TSL:3	n.558+5483A>G		intron	N/A
	LINC01606	ENST00000519314.5	TSL:4	n.491-1523A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25916 AN: 151866 Hom.: 2603 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0806

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.171 AC: 25970 AN: 151986 Hom.: 2620 Cov.: 33 AF XY: 0.170 AC XY: 12593 AN XY: 74292

African (AFR) AF: 0.275 AC: 11347 AN: 41328

American (AMR) AF: 0.127 AC: 1950 AN: 15300

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

East Asian (EAS) AF: 0.138 AC: 713 AN: 5174

South Asian (SAS) AF: 0.0805 AC: 388 AN: 4820

European-Finnish (FIN) AF: 0.167 AC: 1768 AN: 10586

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9024 AN: 67992

Other (OTH) AF: 0.157 AC: 332 AN: 2112

Alfa AF: 0.150 Hom.: 1980

Bravo AF: 0.174

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.92
DANN	Benign	0.30
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7463453; hg19: chr8-58112053;