rs4839200

Variant names:

• chr1-112021228-A-G
• rs4839200
• ENST00000748422.1:n.507-23413T>C

Variant summary

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

The ENST00000748422.1(LINC02884):​n.507-23413T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 152,104 control chromosomes in the GnomAD database, including 47,613 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 0.78 (47613 hom., cov: 32)
• Consequence: LINC02884 ENST00000748422.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 7 publications found

Genes affected

LINC02884 (HGNC:54808): (long intergenic non-protein coding RNA 2884)

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 (NFE) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748422.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02884	ENST00000748422.1		n.507-23413T>C		intron	N/A
	LINC02884	ENST00000748425.1		n.416+3306T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118946 AN: 151986 Hom.: 47599 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.782 AC: 119013 AN: 152104 Hom.: 47613 Cov.: 32 AF XY: 0.772 AC XY: 57377 AN XY: 74326

African (AFR) AF: 0.738 AC: 30614 AN: 41458

American (AMR) AF: 0.651 AC: 9951 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2712 AN: 3470

East Asian (EAS) AF: 0.374 AC: 1934 AN: 5174

South Asian (SAS) AF: 0.675 AC: 3246 AN: 4806

European-Finnish (FIN) AF: 0.783 AC: 8289 AN: 10582

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.875 AC: 59523 AN: 68008

Other (OTH) AF: 0.784 AC: 1658 AN: 2114

Alfa AF: 0.846 Hom.: 102008

Bravo AF: 0.769

Asia WGS AF: 0.512 AC: 1782 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	5.2
DANN	Benign	0.69
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs4839200; hg19: chr1-112563850; COSMIC: COSV59988426;