rs2484992

Positions:

• chr10-31223169-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_134478.1(LINC02664):​n.317+34970T>C variant causes a intron, non coding transcript 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 NR_134478.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02664	NR_134478.1	n.317+34970T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02664	ENST00000605929.1	n.317+34970T>C		intron_variant, non_coding_transcript_variant		2
ZEB1-AS1	ENST00000605946.1	n.178-16687A>G		intron_variant, non_coding_transcript_variant		5
LINC02664	ENST00000662544.1	n.389+16305T>C		intron_variant, non_coding_transcript_variant
LINC02664	ENST00000669722.1	n.608+16305T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.907

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.914

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.990

Gnomad4 OTH AF: 0.839

Alfa AF: 0.859 Hom.: 13161

Bravo AF: 0.774

Asia WGS AF: 0.849 AC: 2952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2484992; hg19: chr10-31512098;