2-34255008-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_126403.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01317	NR_126403.1		n.390-31635G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01320	ENST00000366209.6	TSL:5	n.390-31635G>T		intron	N/A
	LINC01320	ENST00000650021.1		n.63-31635G>T		intron	N/A

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

African (AFR) AF: 0.669 AC: 27697 AN: 41374

American (AMR) AF: 0.793 AC: 12097 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2122 AN: 3468

East Asian (EAS) AF: 0.960 AC: 4937 AN: 5142

South Asian (SAS) AF: 0.836 AC: 4031 AN: 4824

European-Finnish (FIN) AF: 0.692 AC: 7276 AN: 10516

Middle Eastern (MID) AF: 0.640 AC: 187 AN: 292

European-Non Finnish (NFE) AF: 0.720 AC: 48934 AN: 67972

Other (OTH) AF: 0.715 AC: 1505 AN: 2106

Alfa AF: 0.722 Hom.: 139330

Bravo AF: 0.724

Asia WGS AF: 0.845 AC: 2938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.18
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs6733379; hg19: chr2-34480075;