rs17194995

Variant names:

• chr8-57196661-G-T
• rs17194995
• ENST00000518556.5:n.223+2650G>T

Variant summary

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

The ENST00000518556.5(LINC01606):​n.223+2650G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,078 control chromosomes in the GnomAD database, including 1,000 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 0.11 (1000 hom., cov: 32)
• Consequence: LINC01606 ENST00000518556.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.129 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.223+2650G>T		intron_variant	Intron 2 of 2	3
LINC01606	ENST00000519241.6	n.558+2650G>T		intron_variant	Intron 4 of 8	3
LINC01606	ENST00000519314.5	n.490+2650G>T		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17101 AN: 151960 Hom.: 995 Cov.: 32

Gnomad AFR AF: 0.0796

Gnomad AMI AF: 0.0606

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.113 AC: 17123 AN: 152078 Hom.: 1000 Cov.: 32 AF XY: 0.112 AC XY: 8356 AN XY: 74322

African (AFR) AF: 0.0799 AC: 3316 AN: 41492

American (AMR) AF: 0.103 AC: 1572 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0971 AC: 337 AN: 3470

East Asian (EAS) AF: 0.138 AC: 712 AN: 5176

South Asian (SAS) AF: 0.0720 AC: 347 AN: 4822

European-Finnish (FIN) AF: 0.167 AC: 1761 AN: 10526

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8753 AN: 67992

Other (OTH) AF: 0.114 AC: 240 AN: 2110

Alfa AF: 0.120 Hom.: 132

Bravo AF: 0.109

Asia WGS AF: 0.101 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.96
DANN	Benign	0.42
PhyloP100		-1.9
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: rs17194995; hg19: chr8-58109220;