rs11683103

chr2-34687783-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_126404.1(LINC01320):n.371+9856G>A variant causes a intron, non coding transcript 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 NR_126404.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01320	NR_126404.1	n.371+9856G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01320	ENST00000423663.5	n.349+9856G>A		intron_variant, non_coding_transcript_variant		2
LINC01320	ENST00000453774.2	n.93+9856G>A		intron_variant, non_coding_transcript_variant		3
LINC01320	ENST00000604250.3	n.65+9856G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.648

Alfa AF: 0.683 Hom.: 68023

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11683103; hg19: chr2-34912850;