dbSNP rs17427875: HOXA11-AS:n.532A>T (chr7-27185939-A-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

30 publications found

Variant links:

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]

HOXA11-AS links:

ENSG00000278334 (HGNC:):

ENSG00000278334 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000522674.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522674.1. 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
	HOXA11-AS	NR_002795.2		n.532A>T		non_coding_transcript_exon	Exon 1 of 2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
HOXA11-AS	ENST00000522674.1	TSL:1	n.532A>T	non_coding_transcript_exon	Exon 1 of 2
HOXA11-AS	ENST00000520395.2	TSL:2	n.406A>T	non_coding_transcript_exon	Exon 1 of 2
HOXA11-AS	ENST00000522863.2	TSL:5	n.990A>T	non_coding_transcript_exon	Exon 3 of 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

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.0938

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.188

AC:

AN:

European-Finnish (FIN)

AF:

0.227

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.116

AC:

AN:

294

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.151

AC:

22918

AN:

152234

Hom.:

2317

Cov.:

AF XY:

0.155

AC XY:

11527

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.0354

AC:

1472

AN:

41570

American (AMR)

AF:

0.161

AC:

2467

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.246

AC:

854

AN:

3472

East Asian (EAS)

AF:

0.0349

AC:

180

AN:

5158

South Asian (SAS)

AF:

0.256

AC:

1234

AN:

4826

European-Finnish (FIN)

AF:

0.266

AC:

2819

AN:

10598

Middle Eastern (MID)

AF:

0.182

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.196

AC:

13342

AN:

68002

Other (OTH)

AF:

0.155

AC:

328

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

985

1969

2954

3938

4923

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

262

524

786

1048

1310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

6.0

(source)

DANN

Benign

0.89

PhyloP100

0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over