rs10490113

Variant names:

• chr2-59272212-A-C
• rs10490113
• ENST00000409590.1:n.168-5320A>C

Variant summary

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

The ENST00000409590.1(LINC01122):​n.168-5320A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,230 control chromosomes in the GnomAD database, including 1,134 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 0.12 (1134 hom., cov: 32)
• Consequence: LINC01122 ENST00000409590.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 18 publications found

Genes affected

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

ENSG00000233891 (HGNC:):

LINC01793 (HGNC:52583): (long intergenic non-protein coding RNA 1793)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01793	NR_110219.1	n.168-5320A>C		intron_variant	Intron 2 of 2
LOC105374754	XR_002959389.2	n.1448-22519T>G		intron_variant	Intron 1 of 3
LOC105374754	XR_940127.3	n.1618-22519T>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000409590.1	n.168-5320A>C		intron_variant	Intron 2 of 2	2
ENSG00000233891	ENST00000412409.3	n.546-31109T>G		intron_variant	Intron 4 of 4	3
LINC01122	ENST00000422723.6	n.1151-41521A>C		intron_variant	Intron 10 of 10	3

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18081 AN: 152112 Hom.: 1133 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0308

Gnomad EAS AF: 0.0380

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0990

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

GnomAD4 genome AF: 0.119 AC: 18096 AN: 152230 Hom.: 1134 Cov.: 32 AF XY: 0.120 AC XY: 8896 AN XY: 74420

African (AFR) AF: 0.141 AC: 5845 AN: 41538

American (AMR) AF: 0.129 AC: 1965 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0308 AC: 107 AN: 3472

East Asian (EAS) AF: 0.0377 AC: 195 AN: 5176

South Asian (SAS) AF: 0.157 AC: 759 AN: 4824

European-Finnish (FIN) AF: 0.120 AC: 1274 AN: 10594

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7587 AN: 68024

Other (OTH) AF: 0.0975 AC: 206 AN: 2112

Alfa AF: 0.110 Hom.: 2769

Bravo AF: 0.119

Asia WGS AF: 0.0880 AC: 305 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.63
PhyloP100		0.040
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10490113; hg19: chr2-59499347;