rs11683103

Variant names:

• chr2-34687783-G-A
• rs11683103
• ENST00000423663.6:n.546+9856G>A

Variant summary

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

The ENST00000423663.6(LINC01320):​n.546+9856G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,824 control chromosomes in the GnomAD database, including 29,643 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 0.61 (29643 hom., cov: 30)
• Consequence: LINC01320 ENST00000423663.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01320	NR_126404.1	n.371+9856G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01320	ENST00000423663.6	n.546+9856G>A		intron_variant	Intron 1 of 2	2
LINC01320	ENST00000453774.2	n.93+9856G>A		intron_variant	Intron 1 of 4	3
LINC01320	ENST00000604250.4	n.508+9856G>A		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92741 AN: 151706 Hom.: 29607 Cov.: 30

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.611 AC: 92815 AN: 151824 Hom.: 29643 Cov.: 30 AF XY: 0.614 AC XY: 45567 AN XY: 74180

African (AFR) AF: 0.410 AC: 16986 AN: 41380

American (AMR) AF: 0.649 AC: 9892 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2816 AN: 3468

East Asian (EAS) AF: 0.752 AC: 3879 AN: 5160

South Asian (SAS) AF: 0.692 AC: 3331 AN: 4816

European-Finnish (FIN) AF: 0.676 AC: 7093 AN: 10494

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46739 AN: 67952

Other (OTH) AF: 0.648 AC: 1368 AN: 2110

Alfa AF: 0.671 Hom.: 137315

Bravo AF: 0.601

Asia WGS AF: 0.734 AC: 2548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.42
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs11683103; hg19: chr2-34912850;