22-34869265-C-T

Position:

• chr22-34869265-C-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+28571G>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 NR_138042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519

Genes affected

LINC02885 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02885	NR_138042.1	n.460+28571G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02885	ENST00000668433.1	n.343+33358G>A		intron_variant

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

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.588

Alfa AF: 0.567 Hom.: 4155

Bravo AF: 0.634

Asia WGS AF: 0.459 AC: 1597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2038088; hg19: chr22-35265255;