ENST00000685933.2:n.95+17193C>T

Variant names:

• chr1-212267786-G-A
• rs351408
• ENST00000685933.2:n.95+17193C>T

Variant summary

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

The ENST00000685933.2(LINC02608):​n.95+17193C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,092 control chromosomes in the GnomAD database, including 6,946 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 0.29 (6946 hom., cov: 32)
• Consequence: LINC02608 ENST00000685933.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 10 publications found

Genes affected

LINC02608 (HGNC:54052): (long intergenic non-protein coding RNA 2608)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02608	NR_125984.1	n.43+17193C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02608	ENST00000685933.2	n.95+17193C>T		intron_variant	Intron 1 of 4
LINC02608	ENST00000691706.2	n.160+17193C>T		intron_variant	Intron 1 of 2
LINC02608	ENST00000771310.1	n.105+17193C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44024 AN: 151974 Hom.: 6949 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.290 AC: 44045 AN: 152092 Hom.: 6946 Cov.: 32 AF XY: 0.284 AC XY: 21152 AN XY: 74356

African (AFR) AF: 0.173 AC: 7184 AN: 41498

American (AMR) AF: 0.309 AC: 4723 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 776 AN: 3466

East Asian (EAS) AF: 0.204 AC: 1056 AN: 5174

South Asian (SAS) AF: 0.299 AC: 1445 AN: 4826

European-Finnish (FIN) AF: 0.261 AC: 2759 AN: 10564

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.370 AC: 25161 AN: 67966

Other (OTH) AF: 0.302 AC: 638 AN: 2112

Alfa AF: 0.344 Hom.: 6051

Bravo AF: 0.290

Asia WGS AF: 0.239 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.16
DANN	Benign	0.58
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs351408; hg19: chr1-212441128;