2-58510765-C-T

Variant names:

• chr2-58510765-C-T
• rs13387871
• ENST00000422723.5:n.263+82301C>T

Variant summary

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

The ENST00000422723.5(LINC01122):​n.263+82301C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 151,662 control chromosomes in the GnomAD database, including 6,453 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 (6453 hom., cov: 32)
• Consequence: LINC01122 ENST00000422723.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 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
LINC01122	ENST00000422723.5	n.263+82301C>T		intron_variant	Intron 2 of 5	3
LINC01122	ENST00000422793.3	n.121+48920C>T		intron_variant	Intron 2 of 6	5
LINC01122	ENST00000429095.5	n.195+48920C>T		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40705 AN: 151542 Hom.: 6422 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.269 AC: 40784 AN: 151662 Hom.: 6453 Cov.: 32 AF XY: 0.268 AC XY: 19890 AN XY: 74082

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.249

Alfa AF: 0.194 Hom.: 1567

Bravo AF: 0.277

Asia WGS AF: 0.305 AC: 1058 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13387871; hg19: chr2-58737900;