rs12188371

Positions:

• chr5-118428839-C-G

Variant summary

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

The NR_104610.1(LINC02208):​n.2657+39463G>C 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 0.459 in 151,692 control chromosomes in the GnomAD database, including 16,734 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 0.46 (16734 hom., cov: 31)
• Consequence: LINC02208 NR_104610.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02208	NR_104610.1	n.2657+39463G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02208	ENST00000660173.1	n.687+45533G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69638 AN: 151574 Hom.: 16725 Cov.: 31

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.0711

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.459 AC: 69671 AN: 151692 Hom.: 16734 Cov.: 31 AF XY: 0.454 AC XY: 33644 AN XY: 74076

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.0715

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.468

Alfa AF: 0.477 Hom.: 2168

Bravo AF: 0.452

Asia WGS AF: 0.212 AC: 743 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	0.056
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12188371; hg19: chr5-117764534;