rs742295

chr22-34842495-A-Gchr22-34842495-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_138042.1(LINC02885):n.460+55341T>C variant causes a intron, non coding transcript 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 NR_138042.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02885	NR_138042.1	n.460+55341T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02885	ENST00000668433.1	n.343+60128T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.626

Alfa AF: 0.659 Hom.: 4138

Bravo AF: 0.632

Asia WGS AF: 0.481 AC: 1674 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.4
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs742295; hg19: chr22-35238486;