rs742295

Variant names:

• chr22-34842495-A-G
• rs742295
• ENST00000668433.1:n.343+60128T>C

Your query was ambiguous. Multiple possible variants found:

• chr22-34842495-A-G
• chr22-34842495-A-T

Variant summary

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

The ENST00000668433.1(LINC02885):​n.343+60128T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 151,974 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 0.63 (30572 hom., cov: 31)
• Consequence: LINC02885 ENST00000668433.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.689 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02885	NR_138042.1		n.460+55341T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02885	ENST00000668433.1		n.343+60128T>C		intron	N/A
	LINC02885	ENST00000801714.1		n.34+298T>C		intron	N/A
	LINC02885	ENST00000801715.1		n.34+298T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95878 AN: 151856 Hom.: 30579 Cov.: 31

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.631 AC: 95888 AN: 151974 Hom.: 30572 Cov.: 31 AF XY: 0.623 AC XY: 46269 AN XY: 74266

African (AFR) AF: 0.576 AC: 23876 AN: 41440

American (AMR) AF: 0.600 AC: 9160 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2490 AN: 3466

East Asian (EAS) AF: 0.494 AC: 2550 AN: 5164

South Asian (SAS) AF: 0.538 AC: 2587 AN: 4810

European-Finnish (FIN) AF: 0.552 AC: 5824 AN: 10560

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47151 AN: 67948

Other (OTH) AF: 0.626 AC: 1319 AN: 2108

Alfa AF: 0.656 Hom.: 4269

Bravo AF: 0.632

Asia WGS AF: 0.481 AC: 1674 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.55
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs742295; hg19: chr22-35238486;