rs10046044

chr5-118459959-G-Achr5-118459959-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_104610.1(LINC02208):n.2657+8343C>T 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 0.214 in 151,900 control chromosomes in the GnomAD database, including 3,705 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 0.21 (3705 hom., cov: 32)
• Consequence: LINC02208 NR_104610.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02208	NR_104610.1	n.2657+8343C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02208	ENST00000660173.1	n.687+14413C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32476 AN: 151780 Hom.: 3705 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.0487

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.214 AC: 32481 AN: 151900 Hom.: 3705 Cov.: 32 AF XY: 0.208 AC XY: 15462 AN XY: 74238

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.0488

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.227

Alfa AF: 0.244 Hom.: 9618

Bravo AF: 0.217

Asia WGS AF: 0.130 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
Cadd	Benign	11
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10046044; hg19: chr5-117795654;