rs717925

Variant names:

• chr5-159153523-G-C
• rs717925
• ENST00000826187.1:n.208-7826G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000826187.1(LINC02202):​n.208-7826G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 152,332 control chromosomes in the GnomAD database, including 21 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 0.012 (21 hom., cov: 33)
• Consequence: LINC02202 ENST00000826187.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0124 (1882/152332) while in subpopulation NFE AF = 0.0188 (1279/68026). AF 95% confidence interval is 0.0179. There are 21 homozygotes in GnomAd4. There are 884 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 21 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02202	ENST00000826187.1	n.208-7826G>C		intron_variant	Intron 1 of 2
LINC02202	ENST00000826188.1	n.162-7826G>C		intron_variant	Intron 1 of 1
LINC02202	ENST00000826189.1	n.111-7826G>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0124 AC: 1885 AN: 152214 Hom.: 22 Cov.: 33

Gnomad AFR AF: 0.00345

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0135

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0174

Gnomad FIN AF: 0.00433

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0188

Gnomad OTH AF: 0.0172

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

GnomAD4 genome AF: 0.0124 AC: 1882 AN: 152332 Hom.: 21 Cov.: 33 AF XY: 0.0119 AC XY: 884 AN XY: 74486

African (AFR) AF: 0.00344 AC: 143 AN: 41580

American (AMR) AF: 0.0135 AC: 207 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0196 AC: 68 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.0170 AC: 82 AN: 4828

European-Finnish (FIN) AF: 0.00433 AC: 46 AN: 10616

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0188 AC: 1279 AN: 68026

Other (OTH) AF: 0.0170 AC: 36 AN: 2112

Alfa AF: 0.0139 Hom.: 3

Bravo AF: 0.0128

Asia WGS AF: 0.00866 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	9.4
DANN	Benign	0.75
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs717925; hg19: chr5-158580531;