Variant rs17427875 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000522674.1(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
ENST00000522674.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.656

Variant links:

Genes affected

HOXA11-AS (HGNC:):

HOXA11-AS links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Protein	UniProt
HOXA11-AS	NR_002795.2 linkuse as main transcript	n.532A>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
HOXA11-AS	ENST00000522674.1 linkuse as main transcript	n.532A>T	non_coding_transcript_exon_variant	1/2	1
HOXA11-AS	ENST00000520395.2 linkuse as main transcript	n.406A>T	non_coding_transcript_exon_variant	1/2	2
HOXA11-AS	ENST00000522863.2 linkuse as main transcript	n.990A>T	non_coding_transcript_exon_variant	3/5	5

Frequencies

GnomAD3 genomes

AF:

0.151

AC:

22930

AN:

152116

Hom.:

2318

Cov.:

show subpopulations

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:

AN:

388

Hom.:

Cov.:

AF XY:

0.122

AC XY:

AN XY:

238

show subpopulations

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.:

AF XY:

0.155

AC XY:

11527

AN XY:

74430

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over