chr2-58852403-C-T

Variant names:

• chr2-58852403-C-T
• rs4140883
• ENST00000422723.6:n.502+1797C>T

Variant summary

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

The ENST00000422723.6(LINC01122):​n.502+1797C>T variant causes a intron 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 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 2 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=-0.89).
• 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 rank	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.424+1797C>T		intron_variant	Intron 3 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000422723.6	n.502+1797C>T		intron_variant	Intron 4 of 10	3
LINC01122	ENST00000422793.4	n.373+1797C>T		intron_variant	Intron 4 of 6	5
LINC01122	ENST00000427421.5	n.424+1797C>T		intron_variant	Intron 3 of 13	2

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

African (AFR) AF: 0.00980 AC: 407 AN: 41526

American (AMR) AF: 0.0816 AC: 1243 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.0219 AC: 76 AN: 3470

East Asian (EAS) AF: 0.199 AC: 1017 AN: 5122

South Asian (SAS) AF: 0.0659 AC: 318 AN: 4824

European-Finnish (FIN) AF: 0.0421 AC: 446 AN: 10596

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0357 AC: 2422 AN: 67914

Other (OTH) AF: 0.0432 AC: 91 AN: 2108

Alfa AF: 0.0386 Hom.: 229

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs4140883; hg19: chr2-59079538;