rs7843659

Variant names:

• chr8-57187968-T-C
• rs7843659
• ENST00000519241.6:n.432-5917T>C

Variant summary

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

The ENST00000519241.6(LINC01606):​n.432-5917T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,094 control chromosomes in the GnomAD database, including 11,752 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 0.35 (11752 hom., cov: 33)
• Consequence: LINC01606 ENST00000519241.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.760
• Publications: 4 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 = 0.634 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	ENST00000519241.6	n.432-5917T>C		intron_variant	Intron 3 of 8	3
LINC01606	ENST00000519314.5	n.364-5917T>C		intron_variant	Intron 2 of 3	4
LINC01606	ENST00000655105.1	n.350-5917T>C		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52888 AN: 151976 Hom.: 11711 Cov.: 33

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.348 AC: 52982 AN: 152094 Hom.: 11752 Cov.: 33 AF XY: 0.344 AC XY: 25599 AN XY: 74354

African (AFR) AF: 0.640 AC: 26544 AN: 41462

American (AMR) AF: 0.260 AC: 3983 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 839 AN: 3472

East Asian (EAS) AF: 0.167 AC: 863 AN: 5176

South Asian (SAS) AF: 0.192 AC: 924 AN: 4824

European-Finnish (FIN) AF: 0.240 AC: 2542 AN: 10578

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16172 AN: 67980

Other (OTH) AF: 0.348 AC: 733 AN: 2106

Alfa AF: 0.308 Hom.: 1277

Bravo AF: 0.363

Asia WGS AF: 0.219 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.7
DANN	Benign	0.30
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs7843659; hg19: chr8-58100527;