chr22-34975259-G-A

Position:

• chr22-34975259-G-A

Variant summary

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

The NR_138042.1(LINC02885):​n.198+22460C>T 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 0.285 in 152,000 control chromosomes in the GnomAD database, including 6,348 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 0.29 (6348 hom., cov: 32)
• Consequence: LINC02885 NR_138042.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02885	NR_138042.1	n.198+22460C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02885	ENST00000668433.1	n.202+22460C>T		intron_variant, non_coding_transcript_variant
LINC02885	ENST00000700833.1	n.37+22460C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43342 AN: 151882 Hom.: 6349 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.285 AC: 43349 AN: 152000 Hom.: 6348 Cov.: 32 AF XY: 0.283 AC XY: 21004 AN XY: 74290

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.266

Alfa AF: 0.259 Hom.: 1574

Bravo AF: 0.294

Asia WGS AF: 0.259 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.056
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9619497; hg19: chr22-35371248;