rs2161357

Positions:

• chr5-159110111-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_109890.1(LINC02202):​n.357-1748A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,194 control chromosomes in the GnomAD database, including 2,247 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 (2247 hom., cov: 32)
• Consequence: LINC02202 NR_109890.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02202	NR_109890.1	n.357-1748A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02202	ENST00000517335.2	n.357-1765A>G		intron_variant, non_coding_transcript_variant		4
LINC02202	ENST00000499583.1	n.158-1748A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24549 AN: 152076 Hom.: 2244 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0279

Gnomad SAS AF: 0.0736

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.161 AC: 24572 AN: 152194 Hom.: 2247 Cov.: 32 AF XY: 0.161 AC XY: 11968 AN XY: 74384

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.0279

Gnomad4 SAS AF: 0.0736

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.157

Alfa AF: 0.184 Hom.: 3621

Bravo AF: 0.152

Asia WGS AF: 0.0860 AC: 301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2161357; hg19: chr5-158537119;