ENST00000790440.1:n.272G>A

Variant names:

• chr5-17771678-G-A
• rs10805650
• ENST00000790440.1:n.272G>A

Variant summary

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

The ENST00000790440.1(LINC02223):​n.272G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 151,934 control chromosomes in the GnomAD database, including 29,950 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 0.62 (29950 hom., cov: 31)
• Consequence: LINC02223 ENST00000790440.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 3 publications found

Genes affected

LINC02223 (HGNC:53092): (long intergenic non-protein coding RNA 2223)

LOC105374666 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000790440.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02223	ENST00000790440.1		n.272G>A		non_coding_transcript_exon	Exon 3 of 3
	LINC02223	ENST00000511596.5	TSL:5	n.195+2694G>A		intron	N/A
	LINC02223	ENST00000648234.1		n.451+2694G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94254 AN: 151816 Hom.: 29939 Cov.: 31

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.621 AC: 94300 AN: 151934 Hom.: 29950 Cov.: 31 AF XY: 0.619 AC XY: 45971 AN XY: 74232

African (AFR) AF: 0.474 AC: 19610 AN: 41404

American (AMR) AF: 0.609 AC: 9291 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2543 AN: 3470

East Asian (EAS) AF: 0.558 AC: 2877 AN: 5158

South Asian (SAS) AF: 0.634 AC: 3050 AN: 4812

European-Finnish (FIN) AF: 0.695 AC: 7327 AN: 10546

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47376 AN: 67968

Other (OTH) AF: 0.656 AC: 1386 AN: 2114

Alfa AF: 0.645 Hom.: 5275

Bravo AF: 0.609

Asia WGS AF: 0.574 AC: 1996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.77
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10805650; hg19: chr5-17771787;