rs5883064

Positions:

• chr7-27202259-ACT-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_037843.3(HOTTIP):​n.1741_1742del variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 152,042 control chromosomes in the GnomAD database, including 55,535 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.85 (55531 hom., cov: 0)
  • Exomes 𝑓: 0.83 (4 hom.)
• Consequence: HOTTIP NR_037843.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.91

Genes affected

HOTTIP (HGNC:37461): (HOXA distal transcript antisense RNA) This gene produces a long RNA in antisense to the HOXA gene cluster. This transcript may regulate expression of HOXA genes in cis. This gene is upregulated in tumors and is implicated in the promotion of cell proliferation. [provided by RefSeq, Dec 2017]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HOTTIP	NR_037843.3	n.1741_1742del		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HOTTIP	ENST00000521028.4	n.419_420del		non_coding_transcript_exon_variant	1/2	5
HOTTIP	ENST00000472494.1	n.1725_1726del		non_coding_transcript_exon_variant	2/2	2
	ENST00000619957.1			upstream_gene_variant
	ENST00000616633.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129341 AN: 151912 Hom.: 55502 Cov.: 0

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.883

GnomAD4 exome AF: 0.833 AC: 10 AN: 12 Hom.: 4 AF XY: 0.875 AC XY: 7 AN XY: 8

Gnomad4 NFE exome AF: 0.800

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.851 AC: 129423 AN: 152030 Hom.: 55531 Cov.: 0 AF XY: 0.848 AC XY: 63011 AN XY: 74314

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.846

Gnomad4 ASJ AF: 0.960

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.856

Gnomad4 NFE AF: 0.903

Gnomad4 OTH AF: 0.882

Alfa AF: 0.869 Hom.: 7020

Bravo AF: 0.844

Asia WGS AF: 0.780 AC: 2714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5883064; hg19: chr7-27241878;