chr2-58922804-C-G

Variant names:

• chr2-58922804-C-G
• rs10490101
• ENST00000422723.6:n.503-1741C>G

Variant summary

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

The ENST00000422723.6(LINC01122):​n.503-1741C>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 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.675
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000422723.6	n.503-1741C>G		intron_variant	Intron 4 of 10	3
LINC01122	ENST00000422793.4	n.374-1741C>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

African (AFR) AF: 0.0206 AC: 856 AN: 41544

American (AMR) AF: 0.170 AC: 2604 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0812 AC: 282 AN: 3472

East Asian (EAS) AF: 0.445 AC: 2295 AN: 5158

South Asian (SAS) AF: 0.191 AC: 919 AN: 4814

European-Finnish (FIN) AF: 0.0767 AC: 814 AN: 10616

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0948 AC: 6444 AN: 68002

Other (OTH) AF: 0.0986 AC: 208 AN: 2110

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
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs10490101; hg19: chr2-59149939; COSMIC: COSV107521910;