rs13020820

Positions:

• chr2-33755461-G-T

Variant summary

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

The NR_126403.1(LINC01317):​n.68+48508G>T 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 0.285 in 152,160 control chromosomes in the GnomAD database, including 7,779 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 0.28 (7779 hom., cov: 33)
• Consequence: LINC01317 NR_126403.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

Genes affected

LINC01320 (HGNC:50526): (long intergenic non-protein coding RNA 1320)

LINC01317 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01317	NR_126403.1	n.68+48508G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01320	ENST00000366209.6	n.68+48508G>T		intron_variant, non_coding_transcript_variant		5
LINC01320	ENST00000442026.1	n.46+48508G>T		intron_variant, non_coding_transcript_variant		3
LINC01320	ENST00000671333.1	n.69+27827G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43329 AN: 152042 Hom.: 7780 Cov.: 33

Gnomad AFR AF: 0.0734

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.285 AC: 43321 AN: 152160 Hom.: 7779 Cov.: 33 AF XY: 0.281 AC XY: 20915 AN XY: 74390

Gnomad4 AFR AF: 0.0732

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.322

Alfa AF: 0.325 Hom.: 1574

Bravo AF: 0.265

Asia WGS AF: 0.238 AC: 826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.9
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13020820; hg19: chr2-33980528;