10-31239873-T-G

Position:

• chr10-31239873-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_134478.1(LINC02664):​n.318-20109T>G 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 0.856 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 NR_134478.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02664	NR_134478.1	n.318-20109T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02664	ENST00000605929.1	n.318-20109T>G		intron_variant, non_coding_transcript_variant		2
ZEB1-AS1	ENST00000605946.1	n.178-33391A>C		intron_variant, non_coding_transcript_variant		5
LINC02664	ENST00000662544.1	n.390-8654T>G		intron_variant, non_coding_transcript_variant
LINC02664	ENST00000669722.1	n.609-20109T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.926

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.990

Gnomad4 OTH AF: 0.874

Alfa AF: 0.957 Hom.: 23685

Bravo AF: 0.835

Asia WGS AF: 0.864 AC: 2996 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3123688; hg19: chr10-31528802;