chr5-159114192-C-A

Variant names:

• chr5-159114192-C-A
• rs6897374
• ENST00000499583.2:n.351-920C>A

Variant summary

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

The ENST00000499583.2(LINC02202):​n.351-920C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0956 in 152,216 control chromosomes in the GnomAD database, including 928 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 0.096 (928 hom., cov: 32)
• Consequence: LINC02202 ENST00000499583.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.596
• Publications: 6 publications found

Genes affected

LINC02202 (HGNC:53068): (long intergenic non-protein coding RNA 2202)

ENSG00000307478 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02202	NR_109890.1	n.497-920C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02202	ENST00000499583.2	n.351-920C>A		intron_variant	Intron 2 of 2	2
LINC02202	ENST00000517335.3	n.480-920C>A		intron_variant	Intron 2 of 2	4
LINC02202	ENST00000826187.1	n.207+13354C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0956 AC: 14539 AN: 152098 Hom.: 927 Cov.: 32

Gnomad AFR AF: 0.0754

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0665

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0869

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0855

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0956 AC: 14559 AN: 152216 Hom.: 928 Cov.: 32 AF XY: 0.0977 AC XY: 7270 AN XY: 74422

African (AFR) AF: 0.0756 AC: 3141 AN: 41540

American (AMR) AF: 0.106 AC: 1626 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0665 AC: 231 AN: 3472

East Asian (EAS) AF: 0.387 AC: 1999 AN: 5172

South Asian (SAS) AF: 0.113 AC: 543 AN: 4820

European-Finnish (FIN) AF: 0.0869 AC: 921 AN: 10600

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0855 AC: 5817 AN: 68002

Other (OTH) AF: 0.0809 AC: 171 AN: 2114

Alfa AF: 0.0910 Hom.: 3173

Bravo AF: 0.102

Asia WGS AF: 0.189 AC: 656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.8
DANN	Benign	0.75
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs6897374; hg19: chr5-158541200;