rs1250307

Positions:

• chr10-31207045-G-A
• chr10-31207045-G-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+18846G>A 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 0.803 in 152,202 control chromosomes in the GnomAD database, including 54,454 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 (54454 hom., cov: 33)
• Consequence: LINC02664 NR_134478.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363

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=-0.92).
• 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	UniProt
LINC02664	NR_134478.1	n.317+18846G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02664	ENST00000605929.1	n.317+18846G>A		intron_variant, non_coding_transcript_variant		2
ZEB1-AS1	ENST00000605946.1	n.178-563C>T		intron_variant, non_coding_transcript_variant		5
LINC02664	ENST00000662544.1	n.389+181G>A		intron_variant, non_coding_transcript_variant
LINC02664	ENST00000669722.1	n.608+181G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.803 AC: 122173 AN: 152084 Hom.: 54451 Cov.: 33

Gnomad AFR AF: 0.382

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.803 AC: 122187 AN: 152202 Hom.: 54454 Cov.: 33 AF XY: 0.807 AC XY: 60027 AN XY: 74414

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.906

Gnomad4 ASJ AF: 0.891

Gnomad4 EAS AF: 0.806

Gnomad4 SAS AF: 0.914

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.990

Gnomad4 OTH AF: 0.840

Alfa AF: 0.785 Hom.: 2350

Bravo AF: 0.776

Asia WGS AF: 0.848 AC: 2951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1250307; hg19: chr10-31495974;