rs6595142

Variant names:

• chr5-118531496-C-T
• rs6595142
• ENST00000506769.2:n.199-7682G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000506769.2(LINC02208):​n.199-7682G>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 ENST00000506769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506769.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02208	NR_104610.1		n.198-7682G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02208	ENST00000506769.2	TSL:5	n.199-7682G>A		intron	N/A
	LINC02208	ENST00000653787.2		n.203-7682G>A		intron	N/A
	LINC02208	ENST00000654806.1		n.165-7682G>A		intron	N/A

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

African (AFR) AF: 0.913 AC: 37913 AN: 41526

American (AMR) AF: 0.601 AC: 9176 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2318 AN: 3472

East Asian (EAS) AF: 0.107 AC: 549 AN: 5142

South Asian (SAS) AF: 0.443 AC: 2136 AN: 4820

European-Finnish (FIN) AF: 0.588 AC: 6204 AN: 10560

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40490 AN: 67908

Other (OTH) AF: 0.643 AC: 1358 AN: 2112

Alfa AF: 0.620 Hom.: 15998

Bravo AF: 0.673

Asia WGS AF: 0.348 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.082
DANN	Benign	0.22
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs6595142; hg19: chr5-117867191;