rs3908399

Positions:

• chr20-12920627-G-A
• chr20-12920627-G-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PVS1_Moderate BA1

The NR_109868.1(LINC01722):​n.1279+2C>T variant causes a splice donor, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,092 control chromosomes in the GnomAD database, including 3,508 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 0.20 (3508 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC01722 NR_109868.1 splice_donor, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390

Genes affected

LINC01722 (HGNC:52510): (long intergenic non-protein coding RNA 1722)

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01722	NR_109868.1	n.1279+2C>T		splice_donor_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01722	ENST00000456265.1	n.1279+2C>T		splice_donor_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29927 AN: 151974 Hom.: 3507 Cov.: 32

Gnomad AFR AF: 0.0718

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.215

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.197 AC: 29932 AN: 152092 Hom.: 3508 Cov.: 32 AF XY: 0.202 AC XY: 15038 AN XY: 74350

Gnomad4 AFR AF: 0.0718

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.217

Alfa AF: 0.233 Hom.: 2493

Bravo AF: 0.193

Asia WGS AF: 0.196 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.5
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3908399; hg19: chr20-12901275;