10-31223169-T-C

Variant names:

• chr10-31223169-T-C
• rs2484992
• ENST00000605929.1:n.317+34970T>C

Variant summary

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

The ENST00000605929.1(LINC02664):​n.317+34970T>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 152,138 control chromosomes in the GnomAD database, including 54,364 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 (54364 hom., cov: 31)
• Consequence: LINC02664 ENST00000605929.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 5 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=-0.91).
• 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.317+34970T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02664	ENST00000605929.1	TSL:2	n.317+34970T>C		intron	N/A
	ZEB1-AS1	ENST00000605946.1	TSL:5	n.178-16687A>G		intron	N/A
	LINC02664	ENST00000662544.1		n.389+16305T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121913 AN: 152020 Hom.: 54358 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.907

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.801 AC: 121929 AN: 152138 Hom.: 54364 Cov.: 31 AF XY: 0.806 AC XY: 59938 AN XY: 74398

African (AFR) AF: 0.375 AC: 15523 AN: 41448

American (AMR) AF: 0.907 AC: 13847 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3090 AN: 3472

East Asian (EAS) AF: 0.819 AC: 4231 AN: 5168

South Asian (SAS) AF: 0.914 AC: 4411 AN: 4826

European-Finnish (FIN) AF: 0.997 AC: 10578 AN: 10612

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

European-Non Finnish (NFE) AF: 0.990 AC: 67313 AN: 68024

Other (OTH) AF: 0.839 AC: 1772 AN: 2112

Alfa AF: 0.864 Hom.: 23446

Bravo AF: 0.774

Asia WGS AF: 0.849 AC: 2952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.70
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2484992; hg19: chr10-31512098;