rs5883064

Variant names:

• chr7-27202259-ACT-A
• rs5883064
• ENST00000472494.2:n.1736_1737delCT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000472494.2(HOTTIP):​n.1736_1737delCT 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 ENST00000472494.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.91
• Publications: 6 publications found

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]

ENSG00000277469 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000472494.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HOTTIP	NR_037843.3		n.1741_1742delCT		non_coding_transcript_exon	Exon 2 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HOTTIP	ENST00000472494.2	TSL:2	n.1736_1737delCT		non_coding_transcript_exon	Exon 2 of 2
	HOTTIP	ENST00000521028.4	TSL:5	n.419_420delCT		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000277469	ENST00000619957.1	TSL:6	n.-42_-41delCT		upstream_gene	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.800 AC: 8 AN: 10

Other (OTH) AF: 1.00 AC: 2 AN: 2

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

African (AFR) AF: 0.780 AC: 32331 AN: 41464

American (AMR) AF: 0.846 AC: 12934 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.960 AC: 3333 AN: 3472

East Asian (EAS) AF: 0.605 AC: 3094 AN: 5114

South Asian (SAS) AF: 0.913 AC: 4403 AN: 4822

European-Finnish (FIN) AF: 0.856 AC: 9050 AN: 10572

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.903 AC: 61379 AN: 67982

Other (OTH) AF: 0.882 AC: 1860 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.9

Splicing

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

Other links and lift over

dbSNP: rs5883064; hg19: chr7-27241878;