chr2-34080190-G-A

Variant names:

• chr2-34080190-G-A
• rs10495809
• ENST00000366209.6:n.389+135637G>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+135637G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,970 control chromosomes in the GnomAD database, including 8,228 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 0.32 (8228 hom., cov: 32)
• Consequence: LINC01320 ENST00000366209.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• Publications: 17 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01317	NR_126403.1	n.389+135637G>A		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01320	ENST00000366209.6	n.389+135637G>A		intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49093 AN: 151850 Hom.: 8234 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.323 AC: 49098 AN: 151970 Hom.: 8228 Cov.: 32 AF XY: 0.325 AC XY: 24167 AN XY: 74268

African (AFR) AF: 0.249 AC: 10339 AN: 41458

American (AMR) AF: 0.301 AC: 4600 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1489 AN: 3470

East Asian (EAS) AF: 0.461 AC: 2382 AN: 5168

South Asian (SAS) AF: 0.329 AC: 1585 AN: 4816

European-Finnish (FIN) AF: 0.342 AC: 3603 AN: 10546

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23751 AN: 67936

Other (OTH) AF: 0.368 AC: 776 AN: 2108

Alfa AF: 0.348 Hom.: 41419

Bravo AF: 0.321

Asia WGS AF: 0.350 AC: 1221 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	8.3
DANN	Benign	0.53
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs10495809; hg19: chr2-34305257;