rs883834

Variant names:

• chr2-45229972-C-T
• rs883834
• ENST00000378479.5:n.275+24695G>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+24695G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0792 in 152,264 control chromosomes in the GnomAD database, including 513 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 0.079 (513 hom., cov: 32)
• Consequence: LINC01121 ENST00000378479.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345
• Publications: 0 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.125 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+24695G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01121	ENST00000378479.5	TSL:1	n.275+24695G>A		intron	N/A
	LINC01121	ENST00000427020.6	TSL:3	n.705-18312G>A		intron	N/A
	LINC01121	ENST00000430650.2	TSL:3	n.717-37687G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0793 AC: 12065 AN: 152146 Hom.: 515 Cov.: 32

Gnomad AFR AF: 0.0572

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0427

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0959

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0749

Gnomad OTH AF: 0.0780

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

GnomAD4 genome AF: 0.0792 AC: 12065 AN: 152264 Hom.: 513 Cov.: 32 AF XY: 0.0808 AC XY: 6014 AN XY: 74458

African (AFR) AF: 0.0571 AC: 2373 AN: 41552

American (AMR) AF: 0.130 AC: 1984 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0427 AC: 148 AN: 3470

East Asian (EAS) AF: 0.131 AC: 682 AN: 5190

South Asian (SAS) AF: 0.103 AC: 496 AN: 4816

European-Finnish (FIN) AF: 0.0959 AC: 1018 AN: 10610

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.0749 AC: 5091 AN: 68008

Other (OTH) AF: 0.0758 AC: 160 AN: 2112

Alfa AF: 0.0783 Hom.: 1573

Bravo AF: 0.0831

Asia WGS AF: 0.0970 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.71
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs883834;

hg19: chr2-45457111;