rs6729869

Variant names:

• chr2-34060127-T-A
• rs6729869
• ENST00000366209.6:n.389+115574T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000366209.6(LINC01320):​n.389+115574T>A variant causes a intron 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: LINC01320 ENST00000366209.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510
• Publications: 14 publications found

Genes affected

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

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

LOC105374456 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01317	NR_126403.1	n.389+115574T>A		intron_variant	Intron 4 of 6
LOC105374456	XR_939954.2	n.203+5985A>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01320	ENST00000366209.6	n.389+115574T>A		intron_variant	Intron 4 of 5	5
LINC01320	ENST00000442026.1	n.471-623T>A		intron_variant	Intron 5 of 6	3
LINC01320	ENST00000771863.1	n.266-892T>A		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.333 AC: 13805 AN: 41402

American (AMR) AF: 0.351 AC: 5356 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1502 AN: 3472

East Asian (EAS) AF: 0.627 AC: 3242 AN: 5172

South Asian (SAS) AF: 0.398 AC: 1920 AN: 4822

European-Finnish (FIN) AF: 0.397 AC: 4190 AN: 10558

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25110 AN: 67938

Other (OTH) AF: 0.398 AC: 839 AN: 2106

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
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs6729869; hg19: chr2-34285194;