rs10495822

Variant names:

• chr2-34447854-G-T
• rs10495822
• ENST00000422558.1:n.475+63285G>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01320	ENST00000422558.1	n.475+63285G>T		intron_variant	Intron 2 of 2	4
LINC01320	ENST00000650021.1	n.219+63285G>T		intron_variant	Intron 4 of 6
LINC01320	ENST00000654103.1	n.532-28710G>T		intron_variant	Intron 3 of 5

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;