rs10490101

Variant names:

• chr2-58922804-C-G
• rs10490101
• ENST00000422723.5:n.503-1741C>G

Your query was ambiguous. Multiple possible variants found:

• chr2-58922804-C-G
• chr2-58922804-C-T

Variant summary

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

The ENST00000427421.5(LINC01122):​n.453-1741C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0966 in 152,198 control chromosomes in the GnomAD database, including 1,326 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 (1326 hom., cov: 32)
• Consequence: LINC01122 ENST00000427421.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.675

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.453-1741C>G		intron_variant	Intron 4 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000422723.5	n.503-1741C>G		intron_variant	Intron 4 of 5	3
LINC01122	ENST00000422793.3	n.361-1741C>G		intron_variant	Intron 4 of 6	5
LINC01122	ENST00000427421.5	n.453-1741C>G		intron_variant	Intron 4 of 13	2

Frequencies

GnomAD3 genomes AF: 0.0968 AC: 14720 AN: 152080 Hom.: 1329 Cov.: 32

Gnomad AFR AF: 0.0207

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0812

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0767

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0948

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0966 AC: 14707 AN: 152198 Hom.: 1326 Cov.: 32 AF XY: 0.102 AC XY: 7599 AN XY: 74416

Gnomad4 AFR AF: 0.0206

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.0812

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.0767

Gnomad4 NFE AF: 0.0948

Gnomad4 OTH AF: 0.0986

Alfa AF: 0.0848 Hom.: 87

Bravo AF: 0.101

Asia WGS AF: 0.248 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.6
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490101; hg19: chr2-59149939;