rs6749326

Variant names:

• chr2-33750298-G-A
• rs6749326
• ENST00000366209.6:n.68+43345G>A

Variant summary

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

The ENST00000366209.6(LINC01320):​n.68+43345G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 152,022 control chromosomes in the GnomAD database, including 38,518 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 0.70 (38518 hom., cov: 32)
• Consequence: LINC01320 ENST00000366209.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.419
• Publications: 3 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=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000366209.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01317	NR_126403.1		n.68+43345G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01320	ENST00000366209.6	TSL:5	n.68+43345G>A		intron	N/A
	LINC01320	ENST00000442026.1	TSL:3	n.46+43345G>A		intron	N/A
	LINC01320	ENST00000671333.1		n.69+22664G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106594 AN: 151902 Hom.: 38474 Cov.: 32

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.702 AC: 106699 AN: 152022 Hom.: 38518 Cov.: 32 AF XY: 0.700 AC XY: 51988 AN XY: 74302

African (AFR) AF: 0.875 AC: 36305 AN: 41492

American (AMR) AF: 0.721 AC: 11015 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2235 AN: 3468

East Asian (EAS) AF: 0.467 AC: 2409 AN: 5160

South Asian (SAS) AF: 0.635 AC: 3062 AN: 4820

European-Finnish (FIN) AF: 0.599 AC: 6320 AN: 10554

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43299 AN: 67948

Other (OTH) AF: 0.668 AC: 1405 AN: 2102

Alfa AF: 0.654 Hom.: 16744

Bravo AF: 0.716

Asia WGS AF: 0.555 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.0
DANN	Benign	0.76
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs6749326; hg19: chr2-33975365;