2-59055456-T-C

Variant names:

• chr2-59055456-T-C
• rs991964
• ENST00000422723.6:n.1042+32474T>C

Variant summary

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

The ENST00000422723.6(LINC01122):​n.1042+32474T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,922 control chromosomes in the GnomAD database, including 27,322 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 0.58 (27322 hom., cov: 32)
• Consequence: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374
• Publications: 10 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.1273-3105T>C		intron_variant	Intron 12 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000422723.6	n.1042+32474T>C		intron_variant	Intron 9 of 10	3
LINC01122	ENST00000427421.5	n.1273-3105T>C		intron_variant	Intron 12 of 13	2
LINC01122	ENST00000452840.5	n.1054-3105T>C		intron_variant	Intron 10 of 11	5

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87743 AN: 151804 Hom.: 27282 Cov.: 32

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.578 AC: 87843 AN: 151922 Hom.: 27322 Cov.: 32 AF XY: 0.578 AC XY: 42929 AN XY: 74232

African (AFR) AF: 0.820 AC: 34002 AN: 41454

American (AMR) AF: 0.530 AC: 8091 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1713 AN: 3466

East Asian (EAS) AF: 0.644 AC: 3313 AN: 5144

South Asian (SAS) AF: 0.566 AC: 2726 AN: 4820

European-Finnish (FIN) AF: 0.426 AC: 4494 AN: 10552

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31827 AN: 67910

Other (OTH) AF: 0.562 AC: 1185 AN: 2110

Alfa AF: 0.512 Hom.: 65075

Bravo AF: 0.593

Asia WGS AF: 0.601 AC: 2090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.67
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs991964; hg19: chr2-59282591;