rs137270

Positions:

• chr22-34771592-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.461-11105C>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 0.0819 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 NR_138042.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810

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=-0.84).
• 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/exons	MANE	UniProt
LINC02885	NR_138042.1	n.461-11105C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02885	ENST00000668433.1	n.344-12531C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0959

Gnomad4 AMR AF: 0.0679

Gnomad4 ASJ AF: 0.0997

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.0691

Gnomad4 FIN AF: 0.0523

Gnomad4 NFE AF: 0.0755

Gnomad4 OTH AF: 0.0989

Alfa AF: 0.0756 Hom.: 206

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs137270; hg19: chr22-35167583;