rs7719858

Variant names:

• chr5-118559914-C-T
• rs7719858
• ENST00000506769.2:n.198+2007G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000506769.2(LINC02208):​n.198+2007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,082 control chromosomes in the GnomAD database, including 4,278 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 0.23 (4278 hom., cov: 32)
• Consequence: LINC02208 ENST00000506769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 2 publications found

Genes affected

LINC02208 (HGNC:52978): (long intergenic non-protein coding RNA 2208)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02208	NR_104610.1	n.197+2007G>A		intron_variant	Intron 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02208	ENST00000506769.2	n.198+2007G>A		intron_variant	Intron 1 of 8	5
LINC02208	ENST00000515704.1	n.136+2007G>A		intron_variant	Intron 1 of 3	5
LINC02208	ENST00000653787.2	n.202+2007G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34399 AN: 151964 Hom.: 4277 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.00946

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.226 AC: 34435 AN: 152082 Hom.: 4278 Cov.: 32 AF XY: 0.221 AC XY: 16416 AN XY: 74348

African (AFR) AF: 0.294 AC: 12200 AN: 41486

American (AMR) AF: 0.153 AC: 2336 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 838 AN: 3468

East Asian (EAS) AF: 0.00929 AC: 48 AN: 5168

South Asian (SAS) AF: 0.175 AC: 842 AN: 4812

European-Finnish (FIN) AF: 0.184 AC: 1954 AN: 10594

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15534 AN: 67968

Other (OTH) AF: 0.224 AC: 472 AN: 2104

Alfa AF: 0.214 Hom.: 590

Bravo AF: 0.226

Asia WGS AF: 0.114 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	17
DANN	Benign	0.67
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs7719858; hg19: chr5-117895609;