chr2-34059917-G-A

Variant names:

• chr2-34059917-G-A
• rs6711736
• ENST00000366209.6:n.389+115364G>A

Variant summary

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

The ENST00000442026.1(LINC01320):​n.471-833G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 151,974 control chromosomes in the GnomAD database, including 9,475 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 (9475 hom., cov: 32)
• Consequence: LINC01320 ENST00000442026.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559
• 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)

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 = 0.581 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+115364G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01320	ENST00000366209.6	TSL:5	n.389+115364G>A		intron	N/A
	LINC01320	ENST00000442026.1	TSL:3	n.471-833G>A		intron	N/A
	LINC01320	ENST00000771863.1		n.266-1102G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51951 AN: 151856 Hom.: 9477 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.342 AC: 51969 AN: 151974 Hom.: 9475 Cov.: 32 AF XY: 0.347 AC XY: 25798 AN XY: 74266

African (AFR) AF: 0.232 AC: 9631 AN: 41482

American (AMR) AF: 0.344 AC: 5247 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1498 AN: 3470

East Asian (EAS) AF: 0.598 AC: 3081 AN: 5150

South Asian (SAS) AF: 0.398 AC: 1917 AN: 4820

European-Finnish (FIN) AF: 0.396 AC: 4174 AN: 10544

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

European-Non Finnish (NFE) AF: 0.369 AC: 25080 AN: 67928

Other (OTH) AF: 0.374 AC: 787 AN: 2106

Alfa AF: 0.353 Hom.: 12115

Bravo AF: 0.338

Asia WGS AF: 0.443 AC: 1545 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.46
DANN	Benign	0.37
PhyloP100		-0.56

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6711736;

hg19: chr2-34284984;