rs6897374

chr5-159114192-C-A

Variant summary

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

The NR_109890.1(LINC02202):n.497-920C>A 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 0.0956 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 NR_109890.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.596

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=-0.84).
• 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/exons	MANE	UniProt
LINC02202	NR_109890.1	n.497-920C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02202	ENST00000517335.2	n.480-920C>A		intron_variant, non_coding_transcript_variant		4
LINC02202	ENST00000499583.1	n.298-920C>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0756

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0665

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0869

Gnomad4 NFE AF: 0.0855

Gnomad4 OTH AF: 0.0809

Alfa AF: 0.0893 Hom.: 1426

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6897374; hg19: chr5-158541200;