ENST00000668433.1:n.343+33358G>A

Variant names:

• chr22-34869265-C-T
• rs2038088
• ENST00000668433.1:n.343+33358G>A

Variant summary

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

The ENST00000668433.1(LINC02885):​n.343+33358G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,100 control chromosomes in the GnomAD database, including 30,572 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 0.61 (30572 hom., cov: 33)
• Consequence: LINC02885 ENST00000668433.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519
• Publications: 3 publications found

Genes affected

LINC02885 (HGNC:41188): (long intergenic non-protein coding RNA 2885)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668433.1. 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
	LINC02885	NR_138042.1		n.460+28571G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02885	ENST00000668433.1		n.343+33358G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93277 AN: 151982 Hom.: 30533 Cov.: 33

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.614 AC: 93354 AN: 152100 Hom.: 30572 Cov.: 33 AF XY: 0.605 AC XY: 45023 AN XY: 74358

African (AFR) AF: 0.870 AC: 36097 AN: 41500

American (AMR) AF: 0.539 AC: 8237 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2082 AN: 3472

East Asian (EAS) AF: 0.470 AC: 2431 AN: 5170

South Asian (SAS) AF: 0.498 AC: 2403 AN: 4826

European-Finnish (FIN) AF: 0.413 AC: 4367 AN: 10574

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35768 AN: 67960

Other (OTH) AF: 0.588 AC: 1240 AN: 2110

Alfa AF: 0.576 Hom.: 4457

Bravo AF: 0.634

Asia WGS AF: 0.459 AC: 1597 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	4.2
DANN	Benign	0.39
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs2038088; hg19: chr22-35265255;