rs2227072

Variant names:

• chr22-34941769-A-T
• rs2227072
• ENST00000668433.1:n.203-39006T>A

Variant summary

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

The ENST00000668433.1(LINC02885):​n.203-39006T>A variant causes a intron 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 ENST00000668433.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668433.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02885	NR_138042.1		n.199-39006T>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02885	ENST00000668433.1		n.203-39006T>A		intron	N/A
	LINC02885	ENST00000700833.2		n.96-39006T>A		intron	N/A
	LINC02885	ENST00000754702.1		n.366-43813T>A		intron	N/A

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

African (AFR) AF: 0.119 AC: 4789 AN: 40222

American (AMR) AF: 0.465 AC: 7094 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1731 AN: 3470

East Asian (EAS) AF: 0.525 AC: 2711 AN: 5166

South Asian (SAS) AF: 0.663 AC: 3192 AN: 4814

European-Finnish (FIN) AF: 0.551 AC: 5824 AN: 10566

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37904 AN: 67936

Other (OTH) AF: 0.458 AC: 968 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.6
DANN	Benign	0.89
PhyloP100		0.044

Splicing

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

Other links and lift over

dbSNP: rs2227072; hg19: chr22-35337758;