ENST00000452840.5:n.3979G>A

Variant names:

• chr2-59063668-G-A
• rs10490104
• ENST00000452840.5:n.3979G>A

Variant summary

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

The ENST00000452840.5(LINC01122):​n.3979G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0313 in 152,238 control chromosomes in the GnomAD database, including 248 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 0.031 (248 hom., cov: 32)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: LINC01122 ENST00000452840.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.4198G>A		non_coding_transcript_exon_variant	Exon 14 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000452840.5	n.3979G>A		non_coding_transcript_exon_variant	Exon 12 of 12	5
LINC01122	ENST00000422723.6	n.1042+40686G>A		intron_variant	Intron 9 of 10	3
LINC01122	ENST00000650010.2	n.1991+1818G>A		intron_variant	Intron 11 of 14

Frequencies

GnomAD3 genomes AF: 0.0313 AC: 4767 AN: 152114 Hom.: 246 Cov.: 32

Gnomad AFR AF: 0.00792

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0988

Gnomad ASJ AF: 0.00662

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.0474

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0178

Gnomad OTH AF: 0.0302

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0313 AC: 4769 AN: 152232 Hom.: 248 Cov.: 32 AF XY: 0.0340 AC XY: 2531 AN XY: 74428

African (AFR) AF: 0.00790 AC: 328 AN: 41532

American (AMR) AF: 0.0992 AC: 1516 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00662 AC: 23 AN: 3472

East Asian (EAS) AF: 0.240 AC: 1246 AN: 5182

South Asian (SAS) AF: 0.0466 AC: 225 AN: 4824

European-Finnish (FIN) AF: 0.0127 AC: 135 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0178 AC: 1214 AN: 68018

Other (OTH) AF: 0.0332 AC: 70 AN: 2110

Alfa AF: 0.0246 Hom.: 401

Bravo AF: 0.0407

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.56
DANN	Benign	0.57
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs10490104; hg19: chr2-59290803;