rs10495822

chr2-34447854-G-T

Variant summary

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

The ENST00000422558.1(LINC01320):n.475+63285G>T 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 0.27 in 152,064 control chromosomes in the GnomAD database, including 6,839 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 0.27 (6839 hom., cov: 32)
• Consequence: LINC01320 ENST00000422558.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01320	ENST00000422558.1	n.475+63285G>T		intron_variant, non_coding_transcript_variant		4
LINC01320	ENST00000650021.1	n.219+63285G>T		intron_variant, non_coding_transcript_variant
LINC01320	ENST00000654103.1	n.532-28710G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41082 AN: 151946 Hom.: 6838 Cov.: 32

Gnomad AFR AF: 0.0993

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.0276

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.270 AC: 41085 AN: 152064 Hom.: 6839 Cov.: 32 AF XY: 0.269 AC XY: 19993 AN XY: 74322

Gnomad4 AFR AF: 0.0992

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.0273

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.316

Alfa AF: 0.345 Hom.: 17981

Bravo AF: 0.263

Asia WGS AF: 0.126 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.71
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495822; hg19: chr2-34672921;