rs2227072

Positions:

• chr22-34941769-A-T

Variant summary

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

The NR_138042.1(LINC02885):​n.199-39006T>A 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 0.43 in 150,756 control chromosomes in the GnomAD database, including 16,843 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 0.43 (16843 hom., cov: 33)
• Consequence: LINC02885 NR_138042.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440

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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02885	NR_138042.1	n.199-39006T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02885	ENST00000668433.1	n.203-39006T>A		intron_variant, non_coding_transcript_variant
LINC02885	ENST00000700833.1	n.38-39006T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.430 AC: 64836 AN: 150648 Hom.: 16833 Cov.: 33

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.430 AC: 64863 AN: 150756 Hom.: 16843 Cov.: 33 AF XY: 0.436 AC XY: 32128 AN XY: 73662

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.458

Alfa AF: 0.491 Hom.: 2566

Bravo AF: 0.401

Asia WGS AF: 0.603 AC: 2099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.6
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2227072; hg19: chr22-35337758;