rs6595142

Positions:

• chr5-118531496-C-T

Variant summary

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

The NR_104610.1(LINC02208):​n.198-7682G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 152,006 control chromosomes in the GnomAD database, including 35,983 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 0.66 (35983 hom., cov: 33)
• Consequence: LINC02208 NR_104610.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

Genes affected

LINC02208 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02208	NR_104610.1	n.198-7682G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02208	ENST00000506769.1	n.198-7682G>A		intron_variant		5
LINC02208	ENST00000653787.1	n.167-7682G>A		intron_variant
LINC02208	ENST00000654806.1	n.165-7682G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100705 AN: 151888 Hom.: 35927 Cov.: 33

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.663 AC: 100823 AN: 152006 Hom.: 35983 Cov.: 33 AF XY: 0.655 AC XY: 48642 AN XY: 74274

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.643

Alfa AF: 0.618 Hom.: 14231

Bravo AF: 0.673

Asia WGS AF: 0.348 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.082
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6595142; hg19: chr5-117867191;