chr2-34059785-A-G

Variant names:

• chr2-34059785-A-G
• rs9308945
• ENST00000366209.6:n.389+115232A>G

Variant summary

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

The ENST00000442026.1(LINC01320):​n.471-965A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 151,860 control chromosomes in the GnomAD database, including 9,519 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 0.34 (9519 hom., cov: 32)
• Consequence: LINC01320 ENST00000442026.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.85
• Publications: 15 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000442026.1. 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.389+115232A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01320	ENST00000366209.6	TSL:5	n.389+115232A>G		intron	N/A
	LINC01320	ENST00000442026.1	TSL:3	n.471-965A>G		intron	N/A
	LINC01320	ENST00000771863.1		n.266-1234A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52076 AN: 151742 Hom.: 9521 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.343 AC: 52094 AN: 151860 Hom.: 9519 Cov.: 32 AF XY: 0.349 AC XY: 25876 AN XY: 74216

African (AFR) AF: 0.235 AC: 9718 AN: 41426

American (AMR) AF: 0.345 AC: 5261 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1496 AN: 3466

East Asian (EAS) AF: 0.599 AC: 3095 AN: 5164

South Asian (SAS) AF: 0.398 AC: 1916 AN: 4818

European-Finnish (FIN) AF: 0.395 AC: 4156 AN: 10516

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.370 AC: 25107 AN: 67906

Other (OTH) AF: 0.376 AC: 791 AN: 2104

Alfa AF: 0.367 Hom.: 31754

Bravo AF: 0.340

Asia WGS AF: 0.444 AC: 1546 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.0
DANN	Benign	0.38
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs9308945; hg19: chr2-34284852;