22-34943863-T-G

Variant names:

• chr22-34943863-T-G
• rs10483186
• ENST00000668433.1:n.203-41100A>C

Variant summary

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

The ENST00000668433.1(LINC02885):​n.203-41100A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,980 control chromosomes in the GnomAD database, including 20,308 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 0.50 (20308 hom., cov: 32)
• Consequence: LINC02885 ENST00000668433.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02885	NR_138042.1	n.199-41100A>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02885	ENST00000668433.1	n.203-41100A>C		intron_variant	Intron 2 of 3
LINC02885	ENST00000700833.2	n.96-41100A>C		intron_variant	Intron 1 of 3
LINC02885	ENST00000754702.1	n.366-45907A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75931 AN: 151862 Hom.: 20291 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.500 AC: 75995 AN: 151980 Hom.: 20308 Cov.: 32 AF XY: 0.509 AC XY: 37798 AN XY: 74308

African (AFR) AF: 0.300 AC: 12416 AN: 41430

American (AMR) AF: 0.529 AC: 8084 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2001 AN: 3468

East Asian (EAS) AF: 0.603 AC: 3109 AN: 5158

South Asian (SAS) AF: 0.705 AC: 3402 AN: 4826

European-Finnish (FIN) AF: 0.608 AC: 6414 AN: 10548

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.571 AC: 38778 AN: 67962

Other (OTH) AF: 0.522 AC: 1102 AN: 2112

Alfa AF: 0.539 Hom.: 7839

Bravo AF: 0.482

Asia WGS AF: 0.667 AC: 2318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.4
DANN	Benign	0.39
PhyloP100		-0.032

Splicing

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

Other links and lift over

dbSNP: rs10483186; hg19: chr22-35339852;