22-34825836-A-T

Variant names:

• chr22-34825836-A-T
• rs2056965
• ENST00000668433.1:n.344-66775T>A

Variant summary

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

The NR_138042.1(LINC02885):​n.461-65349T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 152,016 control chromosomes in the GnomAD database, including 27,250 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 0.59 (27250 hom., cov: 32)
• Consequence: LINC02885 NR_138042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728

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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02885	NR_138042.1	n.461-65349T>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02885	ENST00000668433.1	n.344-66775T>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90070 AN: 151898 Hom.: 27207 Cov.: 32

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.593 AC: 90167 AN: 152016 Hom.: 27250 Cov.: 32 AF XY: 0.600 AC XY: 44621 AN XY: 74340

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.562

Alfa AF: 0.577 Hom.: 3211

Bravo AF: 0.583

Asia WGS AF: 0.696 AC: 2419 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.53
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: rs2056965; hg19: chr22-35221827;