chr8-57201600-C-T

Variant names:

• chr8-57201600-C-T
• rs6995814
• ENST00000518556.5:n.224-1319C>T

Variant summary

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

The ENST00000518556.5(LINC01606):​n.224-1319C>T 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 151,944 control chromosomes in the GnomAD database, including 2,650 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 (2650 hom., cov: 33)
• Consequence: LINC01606 ENST00000518556.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01606	ENST00000518556.5	TSL:3	n.224-1319C>T		intron	N/A
	LINC01606	ENST00000519241.6	TSL:3	n.558+7589C>T		intron	N/A
	LINC01606	ENST00000521653.6	TSL:4	n.228-6409C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26435 AN: 151826 Hom.: 2633 Cov.: 33

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: 0.0816

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.174 AC: 26490 AN: 151944 Hom.: 2650 Cov.: 33 AF XY: 0.173 AC XY: 12846 AN XY: 74248

African (AFR) AF: 0.286 AC: 11832 AN: 41410

American (AMR) AF: 0.129 AC: 1968 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3468

East Asian (EAS) AF: 0.139 AC: 715 AN: 5158

South Asian (SAS) AF: 0.0815 AC: 392 AN: 4810

European-Finnish (FIN) AF: 0.167 AC: 1763 AN: 10554

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9029 AN: 67970

Other (OTH) AF: 0.161 AC: 340 AN: 2106

Alfa AF: 0.161 Hom.: 271

Bravo AF: 0.177

Asia WGS AF: 0.120 AC: 415 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.14
PhyloP100		-1.4
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: rs6995814; hg19: chr8-58114159;