ENST00000605929.1:n.318-20109T>G

Variant names:

• chr10-31239873-T-G
• rs3123688
• ENST00000605929.1:n.318-20109T>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000605929.1(LINC02664):​n.318-20109T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 152,104 control chromosomes in the GnomAD database, including 58,263 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 0.86 (58263 hom., cov: 32)
• Consequence: LINC02664 ENST00000605929.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 2 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.984 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02664	NR_134478.1		n.318-20109T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02664	ENST00000605929.1	TSL:2	n.318-20109T>G		intron	N/A
	ZEB1-AS1	ENST00000605946.1	TSL:5	n.178-33391A>C		intron	N/A
	LINC02664	ENST00000662544.1		n.390-8654T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130066 AN: 151986 Hom.: 58242 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.856 AC: 130129 AN: 152104 Hom.: 58263 Cov.: 32 AF XY: 0.858 AC XY: 63777 AN XY: 74342

African (AFR) AF: 0.563 AC: 23320 AN: 41452

American (AMR) AF: 0.926 AC: 14144 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3101 AN: 3470

East Asian (EAS) AF: 0.820 AC: 4246 AN: 5180

South Asian (SAS) AF: 0.915 AC: 4401 AN: 4812

European-Finnish (FIN) AF: 0.997 AC: 10583 AN: 10616

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.990 AC: 67320 AN: 67988

Other (OTH) AF: 0.874 AC: 1844 AN: 2110

Alfa AF: 0.958 Hom.: 27313

Bravo AF: 0.835

Asia WGS AF: 0.864 AC: 2996 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	14
DANN	Benign	0.79
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs3123688; hg19: chr10-31528802;