rs13165442

Variant names:

• chr5-159117021-G-C
• rs13165442
• ENST00000499583.2:n.2260G>C

Variant summary

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

The ENST00000499583.2(LINC02202):​n.2260G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,206 control chromosomes in the GnomAD database, including 2,250 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 0.16 (2250 hom., cov: 33)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: LINC02202 ENST00000499583.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02202	NR_109890.1	n.2406G>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02202	ENST00000499583.2	n.2260G>C		non_coding_transcript_exon_variant	Exon 3 of 3	2
LINC02202	ENST00000517335.3	n.2389G>C		non_coding_transcript_exon_variant	Exon 3 of 3	4
LINC02202	ENST00000826187.1	n.207+16183G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24445 AN: 152084 Hom.: 2247 Cov.: 33

Gnomad AFR AF: 0.0976

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.0748

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.156

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.161 AC: 24468 AN: 152202 Hom.: 2250 Cov.: 33 AF XY: 0.160 AC XY: 11923 AN XY: 74400

African (AFR) AF: 0.0978 AC: 4063 AN: 41536

American (AMR) AF: 0.169 AC: 2580 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3468

East Asian (EAS) AF: 0.0285 AC: 148 AN: 5186

South Asian (SAS) AF: 0.0749 AC: 362 AN: 4834

European-Finnish (FIN) AF: 0.255 AC: 2700 AN: 10570

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13572 AN: 68008

Other (OTH) AF: 0.156 AC: 329 AN: 2106

Alfa AF: 0.177 Hom.: 303

Bravo AF: 0.151

Asia WGS AF: 0.0870 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.43
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs13165442; hg19: chr5-158544029;