5-118437000-T-G

Variant names:

• chr5-118437000-T-G
• rs7448017
• ENST00000653787.2:n.721+37372A>C

Variant summary

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

The NR_104610.1(LINC02208):​n.2657+31302A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,116 control chromosomes in the GnomAD database, including 47,226 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 0.78 (47226 hom., cov: 32)
• Consequence: LINC02208 NR_104610.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_104610.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02208	NR_104610.1		n.2657+31302A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02208	ENST00000653787.2		n.721+37372A>C		intron	N/A
	LINC02208	ENST00000654806.1		n.810+35063A>C		intron	N/A
	LINC02208	ENST00000659234.1		n.890+35063A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118652 AN: 151998 Hom.: 47194 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.781 AC: 118731 AN: 152116 Hom.: 47226 Cov.: 32 AF XY: 0.781 AC XY: 58078 AN XY: 74358

African (AFR) AF: 0.632 AC: 26208 AN: 41482

American (AMR) AF: 0.860 AC: 13147 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3085 AN: 3472

East Asian (EAS) AF: 0.979 AC: 5074 AN: 5182

South Asian (SAS) AF: 0.901 AC: 4345 AN: 4822

European-Finnish (FIN) AF: 0.754 AC: 7960 AN: 10564

Middle Eastern (MID) AF: 0.856 AC: 250 AN: 292

European-Non Finnish (NFE) AF: 0.826 AC: 56135 AN: 67998

Other (OTH) AF: 0.803 AC: 1694 AN: 2110

Alfa AF: 0.816 Hom.: 80680

Bravo AF: 0.782

Asia WGS AF: 0.925 AC: 3212 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.21
DANN	Benign	0.40
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7448017; hg19: chr5-117772695;