10-31226203-T-C

Variant names:

• chr10-31226203-T-C
• rs2484990
• ENST00000605929.1:n.318-33779T>C

Variant summary

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

The ENST00000605929.1(LINC02664):​n.318-33779T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,176 control chromosomes in the GnomAD database, including 54,366 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 0.80 (54366 hom., cov: 32)
• Consequence: LINC02664 ENST00000605929.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453
• Publications: 6 publications found

Genes affected

LINC02664 (HGNC:54150): (long intergenic non-protein coding RNA 2664)

ZEB1-AS1 (HGNC:42354): (ZEB1 antisense RNA 1) This locus produces long non-coding RNA that is transcribed from a shared bi-directional promoter with zinc finger E-box binding homeobox 1 (ZEB1). This transcript binds lysine methyltransferase 2A and promotes histone modifications that are thought to promote expression of ZEB1. Expression of this gene is correlated with tumor progression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2017]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000605929.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02664	NR_134478.1		n.318-33779T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02664	ENST00000605929.1	TSL:2	n.318-33779T>C		intron	N/A
	ZEB1-AS1	ENST00000605946.1	TSL:5	n.178-19721A>G		intron	N/A
	LINC02664	ENST00000662544.1		n.389+19339T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121921 AN: 152058 Hom.: 54360 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.801 AC: 121937 AN: 152176 Hom.: 54366 Cov.: 32 AF XY: 0.805 AC XY: 59935 AN XY: 74408

African (AFR) AF: 0.374 AC: 15518 AN: 41454

American (AMR) AF: 0.906 AC: 13876 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3089 AN: 3470

East Asian (EAS) AF: 0.817 AC: 4236 AN: 5182

South Asian (SAS) AF: 0.914 AC: 4404 AN: 4820

European-Finnish (FIN) AF: 0.997 AC: 10577 AN: 10610

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.990 AC: 67302 AN: 68012

Other (OTH) AF: 0.838 AC: 1771 AN: 2114

Alfa AF: 0.722 Hom.: 17414

Bravo AF: 0.774

Asia WGS AF: 0.849 AC: 2951 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	7.3
DANN	Benign	0.94
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs2484990; hg19: chr10-31515132;