rs17427875

chr7-27185939-A-T

Variant summary

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

The NR_002795.2(HOXA11-AS):n.532A>T 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 0.15 in 152,622 control chromosomes in the GnomAD database, including 2,318 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 0.15 (2317 hom., cov: 33)
  • Exomes 𝑓: 0.12 (1 hom.)
• Consequence: HOXA11-AS NR_002795.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.656

Genes affected

HOXA11-AS (HGNC:24957): (HOXA11 antisense RNA) This gene produces a long non-coding RNA in antisense to transcription of the homeobox A11 gene. This transcript may associate with chromatin factors such as Polycomb repressive complex and act as a sponge for microRNAs, thereby participating in the regulation of expression of target genes. High levels of this transcript may be associated with tumor progression. [provided by RefSeq, Dec 2017]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HOXA11-AS	NR_002795.2	n.532A>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000615604.1	n.108A>T		non_coding_transcript_exon_variant	1/1
HOXA11-AS	ENST00000520360.6	n.579-170A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22930 AN: 152116 Hom.: 2318 Cov.: 33

Gnomad AFR AF: 0.0355

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.0352

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.156

GnomAD4 exome AF: 0.116 AC: 45 AN: 388 Hom.: 1 Cov.: 0 AF XY: 0.122 AC XY: 29 AN XY: 238

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0938

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.188

Gnomad4 FIN exome AF: 0.227

Gnomad4 NFE exome AF: 0.116

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.151 AC: 22918 AN: 152234 Hom.: 2317 Cov.: 33 AF XY: 0.155 AC XY: 11527 AN XY: 74430

Gnomad4 AFR AF: 0.0354

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.0349

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.155

Alfa AF: 0.170 Hom.: 338

Bravo AF: 0.131

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
Cadd	Benign	6.0
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17427875; hg19: chr7-27225558;