rs7719858

chr5-118559914-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_104610.1(LINC02208):n.197+2007G>A variant causes a intron, non coding transcript 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 NR_104610.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02208	NR_104610.1	n.197+2007G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02208	ENST00000660173.1	n.168+2007G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.00929

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.224

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7719858; hg19: chr5-117895609;