rs10490096

Variant names:

• chr2-58842794-C-T
• rs10490096
• ENST00000422723.6:n.326-7636C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000422723.6(LINC01122):​n.326-7636C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0973 in 151,984 control chromosomes in the GnomAD database, including 970 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 0.097 (970 hom., cov: 32)
• Consequence: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 3 publications found

Genes affected

LINC01122 (HGNC:49267): (long intergenic non-protein coding RNA 1122)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.248-7636C>T		intron_variant	Intron 2 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000422723.6	n.326-7636C>T		intron_variant	Intron 3 of 10	3
LINC01122	ENST00000422793.4	n.197-7636C>T		intron_variant	Intron 3 of 6	5
LINC01122	ENST00000427421.5	n.248-7636C>T		intron_variant	Intron 2 of 13	2

Frequencies

GnomAD3 genomes AF: 0.0974 AC: 14789 AN: 151866 Hom.: 971 Cov.: 32

Gnomad AFR AF: 0.0251

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.00252

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0973 AC: 14790 AN: 151984 Hom.: 970 Cov.: 32 AF XY: 0.0970 AC XY: 7209 AN XY: 74294

African (AFR) AF: 0.0250 AC: 1038 AN: 41534

American (AMR) AF: 0.126 AC: 1915 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 492 AN: 3462

East Asian (EAS) AF: 0.00253 AC: 13 AN: 5140

South Asian (SAS) AF: 0.172 AC: 829 AN: 4818

European-Finnish (FIN) AF: 0.103 AC: 1093 AN: 10612

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8937 AN: 67866

Other (OTH) AF: 0.103 AC: 218 AN: 2110

Alfa AF: 0.129 Hom.: 726

Bravo AF: 0.0948

Asia WGS AF: 0.0710 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	17
DANN	Benign	0.63
PhyloP100		1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10490096; hg19: chr2-59069929;