rs1314004

Variant names:

• chr10-31255097-A-G
• rs1314004
• ENST00000605929.1:n.318-4885A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-31255097-A-G
• chr10-31255097-A-T

Variant summary

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

The ENST00000605929.1(LINC02664):​n.318-4885A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 151,724 control chromosomes in the GnomAD database, including 45,486 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 0.76 (45486 hom., cov: 30)
• Consequence: LINC02664 ENST00000605929.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166

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=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02664	NR_134478.1	n.318-4885A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02664	ENST00000605929.1	n.318-4885A>G		intron_variant	Intron 1 of 1	2
ZEB1-AS1	ENST00000605946.1	n.178-48615T>C		intron_variant	Intron 1 of 1	5
LINC02664	ENST00000662544.1	n.457-4885A>G		intron_variant	Intron 3 of 4
LINC02664	ENST00000669722.1	n.609-4885A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.765 AC: 115912 AN: 151606 Hom.: 45433 Cov.: 30

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.765 AC: 116024 AN: 151724 Hom.: 45486 Cov.: 30 AF XY: 0.763 AC XY: 56579 AN XY: 74128

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.771

Gnomad4 EAS AF: 0.907

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.778

Alfa AF: 0.699 Hom.: 45100

Bravo AF: 0.768

Asia WGS AF: 0.866 AC: 3010 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	8.1
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1314004; hg19: chr10-31544026;