22-34994317-C-T

Variant names:

• chr22-34994317-C-T
• rs9610191
• ENST00000668433.1:n.202+3402G>A

Variant summary

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

The ENST00000668433.1(LINC02885):​n.202+3402G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0988 in 152,148 control chromosomes in the GnomAD database, including 876 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 0.099 (876 hom., cov: 32)
• Consequence: LINC02885 ENST00000668433.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 6 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02885	NR_138042.1	n.198+3402G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02885	ENST00000668433.1	n.202+3402G>A		intron_variant	Intron 2 of 3
LINC02885	ENST00000700833.2	n.95+3402G>A		intron_variant	Intron 1 of 3
LINC02885	ENST00000754702.1	n.365+3402G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0987 AC: 15008 AN: 152030 Hom.: 877 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.0670

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.0859

Gnomad SAS AF: 0.0843

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0781

Gnomad OTH AF: 0.0962

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

GnomAD4 genome AF: 0.0988 AC: 15029 AN: 152148 Hom.: 876 Cov.: 32 AF XY: 0.100 AC XY: 7469 AN XY: 74366

African (AFR) AF: 0.136 AC: 5657 AN: 41506

American (AMR) AF: 0.0669 AC: 1022 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3470

East Asian (EAS) AF: 0.0857 AC: 442 AN: 5158

South Asian (SAS) AF: 0.0845 AC: 408 AN: 4826

European-Finnish (FIN) AF: 0.155 AC: 1642 AN: 10578

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0781 AC: 5315 AN: 68012

Other (OTH) AF: 0.0952 AC: 201 AN: 2112

Alfa AF: 0.0843 Hom.: 92

Bravo AF: 0.0936

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.41
DANN	Benign	0.71
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs9610191; hg19: chr22-35390306;