rs1346007

Positions:

• chr2-34080492-C-A
• chr2-34080492-C-G

Variant summary

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

The NR_126403.1(LINC01317):​n.389+135939C>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 0.278 in 151,958 control chromosomes in the GnomAD database, including 6,343 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 (6343 hom., cov: 32)
• Consequence: LINC01317 NR_126403.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01317	NR_126403.1	n.389+135939C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01320	ENST00000366209.6	n.389+135939C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42193 AN: 151840 Hom.: 6350 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.278 AC: 42197 AN: 151958 Hom.: 6343 Cov.: 32 AF XY: 0.284 AC XY: 21109 AN XY: 74280

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.319

Alfa AF: 0.258 Hom.: 2475

Bravo AF: 0.277

Asia WGS AF: 0.408 AC: 1424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	13
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1346007; hg19: chr2-34305559;