2-59082913-C-T

Variant names:

• chr2-59082913-C-T
• rs2192497
• ENST00000422723.6:n.1043-53206C>T

Variant summary

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

The ENST00000422723.6(LINC01122):​n.1043-53206C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 152,160 control chromosomes in the GnomAD database, including 48,628 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 0.79 (48628 hom., cov: 32)
• Consequence: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422723.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01122	ENST00000422723.6	TSL:3	n.1043-53206C>T		intron	N/A
	LINC01122	ENST00000650010.2		n.1991+21063C>T		intron	N/A
	LINC01122	ENST00000715766.1		n.914-53206C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120489 AN: 152042 Hom.: 48579 Cov.: 32

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.793 AC: 120594 AN: 152160 Hom.: 48628 Cov.: 32 AF XY: 0.796 AC XY: 59172 AN XY: 74380

African (AFR) AF: 0.914 AC: 37983 AN: 41546

American (AMR) AF: 0.821 AC: 12540 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2328 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5155 AN: 5166

South Asian (SAS) AF: 0.831 AC: 4000 AN: 4816

European-Finnish (FIN) AF: 0.755 AC: 7991 AN: 10588

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48295 AN: 67984

Other (OTH) AF: 0.749 AC: 1581 AN: 2112

Alfa AF: 0.757 Hom.: 17472

Bravo AF: 0.803

Asia WGS AF: 0.896 AC: 3115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.56
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2192497; hg19: chr2-59310048;