rs137270

Variant names:

• chr22-34771592-G-A
• rs137270
• ENST00000668433.1:n.344-12531C>T

Variant summary

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

The ENST00000668433.1(LINC02885):​n.344-12531C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0819 in 152,120 control chromosomes in the GnomAD database, including 600 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 0.082 (600 hom., cov: 32)
• Consequence: LINC02885 ENST00000668433.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 3 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02885	NR_138042.1	n.461-11105C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02885	ENST00000668433.1	n.344-12531C>T		intron_variant	Intron 3 of 3
LINC02885	ENST00000801714.1	n.35-11105C>T		intron_variant	Intron 1 of 2
LINC02885	ENST00000801715.1	n.35-11105C>T		intron_variant	Intron 1 of 2
LINC02885	ENST00000801716.1	n.31-11105C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0819 AC: 12442 AN: 152002 Hom.: 597 Cov.: 32

Gnomad AFR AF: 0.0958

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0681

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0699

Gnomad FIN AF: 0.0523

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0755

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.0819 AC: 12453 AN: 152120 Hom.: 600 Cov.: 32 AF XY: 0.0807 AC XY: 6000 AN XY: 74356

African (AFR) AF: 0.0959 AC: 3979 AN: 41510

American (AMR) AF: 0.0679 AC: 1037 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0997 AC: 346 AN: 3470

East Asian (EAS) AF: 0.140 AC: 722 AN: 5156

South Asian (SAS) AF: 0.0691 AC: 333 AN: 4816

European-Finnish (FIN) AF: 0.0523 AC: 554 AN: 10596

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0755 AC: 5133 AN: 67972

Other (OTH) AF: 0.0989 AC: 209 AN: 2114

Alfa AF: 0.0762 Hom.: 239

Bravo AF: 0.0859

Asia WGS AF: 0.122 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.88
DANN	Benign	0.60
PhyloP100		0.081

Splicing

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

Other links and lift over

dbSNP: rs137270; hg19: chr22-35167583;