2-58921975-T-A

Position:

• chr2-58921975-T-A

Variant summary

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

The NR_033873.1(LINC01122):​n.453-2570T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,948 control chromosomes in the GnomAD database, including 18,746 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 0.49 (18746 hom., cov: 31)
• Consequence: LINC01122 NR_033873.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.453-2570T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000452840.5	n.435-2570T>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74651 AN: 151830 Hom.: 18730 Cov.: 31

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.492 AC: 74707 AN: 151948 Hom.: 18746 Cov.: 31 AF XY: 0.492 AC XY: 36560 AN XY: 74264

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.480

Alfa AF: 0.312 Hom.: 735

Bravo AF: 0.499

Asia WGS AF: 0.538 AC: 1872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.9
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6545708; hg19: chr2-59149110;