rs4140883

chr2-58852403-C-T

Variant summary

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

The NR_033873.1(LINC01122):n.424+1797C>T 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 0.0397 in 151,994 control chromosomes in the GnomAD database, including 246 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 0.040 (246 hom., cov: 32)
• Consequence: LINC01122 NR_033873.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01122	NR_033873.1	n.424+1797C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01122	ENST00000452840.5	n.434+1797C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0397 AC: 6035 AN: 151876 Hom.: 244 Cov.: 32

Gnomad AFR AF: 0.00983

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0811

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.0669

Gnomad FIN AF: 0.0421

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0357

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0397 AC: 6031 AN: 151994 Hom.: 246 Cov.: 32 AF XY: 0.0418 AC XY: 3105 AN XY: 74278

Gnomad4 AFR AF: 0.00980

Gnomad4 AMR AF: 0.0816

Gnomad4 ASJ AF: 0.0219

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.0659

Gnomad4 FIN AF: 0.0421

Gnomad4 NFE AF: 0.0357

Gnomad4 OTH AF: 0.0432

Alfa AF: 0.0389 Hom.: 179

Bravo AF: 0.0429

Asia WGS AF: 0.113 AC: 394 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.9
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4140883; hg19: chr2-59079538;