2-34060127-T-A

Position:

• chr2-34060127-T-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+115574T>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 0.372 in 151,922 control chromosomes in the GnomAD database, including 10,819 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 0.37 (10819 hom., cov: 32)
• Consequence: LINC01317 NR_126403.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01317	NR_126403.1	n.389+115574T>A		intron_variant, non_coding_transcript_variant
LOC105374456	XR_939954.2	n.203+5985A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01320	ENST00000366209.6	n.389+115574T>A		intron_variant, non_coding_transcript_variant		5
LINC01320	ENST00000442026.1	n.471-623T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56500 AN: 151804 Hom.: 10822 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.372 AC: 56517 AN: 151922 Hom.: 10819 Cov.: 32 AF XY: 0.377 AC XY: 27980 AN XY: 74248

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.398

Alfa AF: 0.362 Hom.: 1246

Bravo AF: 0.372

Asia WGS AF: 0.461 AC: 1608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.6
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6729869; hg19: chr2-34285194;