2-59075742-T-C

Variant names:

• chr2-59075742-T-C
• rs887912
• ENST00000422723.6:n.1042+52760T>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+52760T>C 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 152,058 control chromosomes in the GnomAD database, including 48,630 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 (48630 hom., cov: 32)
• Consequence: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 122 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=-0.85).
• 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.1042+52760T>C		intron	N/A
	LINC01122	ENST00000650010.2		n.1991+13892T>C		intron	N/A
	LINC01122	ENST00000715766.1		n.913+52760T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120479 AN: 151940 Hom.: 48581 Cov.: 32

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.793 AC: 120585 AN: 152058 Hom.: 48630 Cov.: 32 AF XY: 0.796 AC XY: 59184 AN XY: 74346

African (AFR) AF: 0.912 AC: 37833 AN: 41502

American (AMR) AF: 0.822 AC: 12544 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2336 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5159 AN: 5170

South Asian (SAS) AF: 0.836 AC: 4025 AN: 4814

European-Finnish (FIN) AF: 0.754 AC: 7973 AN: 10568

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48405 AN: 67956

Other (OTH) AF: 0.750 AC: 1586 AN: 2114

Alfa AF: 0.731 Hom.: 65919

Bravo AF: 0.803

Asia WGS AF: 0.899 AC: 3126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.62
DANN	Benign	0.50
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs887912; hg19: chr2-59302877;