rs6995814

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01606	ENST00000518556.5	n.224-1319C>T		intron_variant	Intron 2 of 2	3
LINC01606	ENST00000519241.6	n.558+7589C>T		intron_variant	Intron 4 of 8	3
LINC01606	ENST00000521653.6	n.228-6409C>T		intron_variant	Intron 2 of 6	4

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

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.0815

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.161

Alfa AF: 0.156 Hom.: 240

Bravo AF: 0.177

Asia WGS AF: 0.120 AC: 415 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6995814; hg19: chr8-58114159;