2-34255008-G-T

Variant names:

• chr2-34255008-G-T
• rs6733379
• ENST00000366209.6:n.390-31635G>T

Variant summary

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

The NR_126403.1(LINC01317):​n.390-31635G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 151,866 control chromosomes in the GnomAD database, including 39,706 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 0.72 (39706 hom., cov: 30)
• Consequence: LINC01317 NR_126403.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.602

Genes affected

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

LINC01317 (HGNC:50523): (long intergenic non-protein coding RNA 1317)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01317	NR_126403.1	n.390-31635G>T		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01320	ENST00000366209.6	n.390-31635G>T		intron_variant	Intron 4 of 5	5
LINC01320	ENST00000650021.1	n.63-31635G>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109356 AN: 151746 Hom.: 39671 Cov.: 30

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.641

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.721 AC: 109450 AN: 151866 Hom.: 39706 Cov.: 30 AF XY: 0.723 AC XY: 53660 AN XY: 74220

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.793

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.715

Alfa AF: 0.722 Hom.: 63065

Bravo AF: 0.724

Asia WGS AF: 0.845 AC: 2938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6733379; hg19: chr2-34480075;