Genetic Variant HOXC13-AS:n.594A>G (chr12-53936191-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000512916.3(HOXC13-AS):n.594A>G 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 0.59 in 152,014 control chromosomes in the GnomAD database, including 28,727 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 0.59 ( 28714 hom., cov: 31)

Exomes 𝑓: 0.71 ( 13 hom. )

Consequence

HOXC13-AS
ENST00000512916.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.41

Publications

12 publications found

Variant links:

Genes affected

HOXC13-AS (HGNC:43753): (HOXC13 antisense RNA)

HOXC13-AS links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HOXC13-AS	NR_047507.1 link	n.545A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HOXC13-AS	ENST00000512916.3 link	n.594A>G	non_coding_transcript_exon_variant	Exon 3 of 3	3
HOXC13-AS	ENST00000810610.1 link	n.534A>G	non_coding_transcript_exon_variant	Exon 3 of 3
HOXC13-AS	ENST00000810611.1 link	n.978A>G	non_coding_transcript_exon_variant	Exon 3 of 3
HOXC13-AS	ENST00000810609.1 link	n.375-33A>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.590

AC:

89603

AN:

151846

Hom.:

28713

Cov.:

show subpopulations

Gnomad AFR

AF:

0.326

Gnomad AMI

AF:

0.686

Gnomad AMR

AF:

0.719

Gnomad ASJ

AF:

0.569

Gnomad EAS

AF:

0.785

Gnomad SAS

AF:

0.440

Gnomad FIN

AF:

0.690

Gnomad MID

AF:

0.547

Gnomad NFE

AF:

0.701

Gnomad OTH

AF:

0.603

GnomAD4 exome

AF:

0.708

AC:

AN:

Hom.:

Cov.:

AF XY:

0.789

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.625

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.725

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.406

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:

0.590

AC:

89611

AN:

151966

Hom.:

28714

Cov.:

AF XY:

0.592

AC XY:

43949

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.326

AC:

13488

AN:

41416

American (AMR)

AF:

0.720

AC:

11003

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.569

AC:

1974

AN:

3470

East Asian (EAS)

AF:

0.784

AC:

4028

AN:

5136

South Asian (SAS)

AF:

0.441

AC:

2123

AN:

4814

European-Finnish (FIN)

AF:

0.690

AC:

7270

AN:

10542

Middle Eastern (MID)

AF:

0.531

AC:

156

AN:

294

European-Non Finnish (NFE)

AF:

0.701

AC:

47685

AN:

67986

Other (OTH)

AF:

0.597

AC:

1258

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1687

3375

5062

6750

8437

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

738

1476

2214

2952

3690

<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:

0.661

Hom.:

120092

Bravo

AF:

0.588

Asia WGS

AF:

0.538

AC:

1873

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.0

(source)

DANN

Benign

0.59

PhyloP100

-1.4

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over