chr2-34017935-C-A

Position:

• chr2-34017935-C-A

Variant summary

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

The NR_126403.1(LINC01317):​n.389+73382C>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 0.343 in 151,856 control chromosomes in the GnomAD database, including 9,511 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 0.34 (9511 hom., cov: 31)
• Consequence: LINC01317 NR_126403.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01317	NR_126403.1	n.389+73382C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01320	ENST00000366209.6	n.389+73382C>A		intron_variant, non_coding_transcript_variant		5
LINC01320	ENST00000442026.1	n.471-42815C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52090 AN: 151736 Hom.: 9512 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.343 AC: 52083 AN: 151856 Hom.: 9511 Cov.: 31 AF XY: 0.349 AC XY: 25871 AN XY: 74196

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.375

Alfa AF: 0.355 Hom.: 1241

Bravo AF: 0.326

Asia WGS AF: 0.362 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495803; hg19: chr2-34243002;