rs12188371

Variant names:

• chr5-118428839-C-G
• rs12188371
• ENST00000653787.2:n.721+45533G>C

Variant summary

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

The ENST00000653787.2(LINC02208):​n.721+45533G>C variant causes a intron 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 ENST00000653787.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 3 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=-0.92).
• 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 rank	MANE	Protein	UniProt
LINC02208	NR_104610.1	n.2657+39463G>C		intron_variant	Intron 9 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02208	ENST00000653787.2	n.721+45533G>C		intron_variant	Intron 5 of 5
LINC02208	ENST00000654806.1	n.810+43224G>C		intron_variant	Intron 6 of 6
LINC02208	ENST00000659234.1	n.890+43224G>C		intron_variant	Intron 8 of 8

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

African (AFR) AF: 0.468 AC: 19351 AN: 41336

American (AMR) AF: 0.404 AC: 6144 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1939 AN: 3470

East Asian (EAS) AF: 0.0715 AC: 369 AN: 5164

South Asian (SAS) AF: 0.295 AC: 1416 AN: 4796

European-Finnish (FIN) AF: 0.465 AC: 4868 AN: 10476

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34047 AN: 67922

Other (OTH) AF: 0.468 AC: 983 AN: 2100

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs12188371; hg19: chr5-117764534;