chr2-45233954-C-T

Variant names:

• chr2-45233954-C-T
• rs2194398
• ENST00000378479.5:n.275+20713G>A

Variant summary

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

The ENST00000378479.5(LINC01121):​n.275+20713G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 152,228 control chromosomes in the GnomAD database, including 57,461 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 0.87 (57461 hom., cov: 33)
• Consequence: LINC01121 ENST00000378479.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698
• Publications: 1 publications found

Genes affected

LINC01121 (HGNC:49266): (long intergenic non-protein coding RNA 1121)

ENSG00000286728 (HGNC:):

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 = 0.928 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000378479.5. 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
	LINC01121	NR_033831.1		n.275+20713G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01121	ENST00000378479.5	TSL:1	n.275+20713G>A		intron	N/A
	LINC01121	ENST00000427020.6	TSL:3	n.705-22294G>A		intron	N/A
	LINC01121	ENST00000430650.2	TSL:3	n.717-41669G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.867 AC: 131897 AN: 152110 Hom.: 57421 Cov.: 33

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.867 AC: 131993 AN: 152228 Hom.: 57461 Cov.: 33 AF XY: 0.865 AC XY: 64365 AN XY: 74424

African (AFR) AF: 0.936 AC: 38878 AN: 41546

American (AMR) AF: 0.870 AC: 13309 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2698 AN: 3472

East Asian (EAS) AF: 0.890 AC: 4612 AN: 5182

South Asian (SAS) AF: 0.839 AC: 4048 AN: 4826

European-Finnish (FIN) AF: 0.821 AC: 8689 AN: 10580

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57033 AN: 68000

Other (OTH) AF: 0.853 AC: 1802 AN: 2112

Alfa AF: 0.851 Hom.: 7154

Bravo AF: 0.876

Asia WGS AF: 0.858 AC: 2984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.27
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs2194398; hg19: chr2-45461093;