Variant 12-53938949-C-CTTA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PM4_SupportingBP6_ModerateBA1

The NM_017410.3(HOXC13):c.45_47dupTAT(p.Leu15_Met16insIle) variant causes a disruptive inframe insertion change. The variant allele was found at a frequency of 0.0208 in 1,558,642 control chromosomes in the GnomAD database, including 614 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.016 ( 42 hom., cov: 32)

Exomes 𝑓: 0.021 ( 572 hom. )

Consequence

HOXC13
NM_017410.3 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 6.86

Variant links:

Genes affected

HOXC13 (HGNC:5125): (homeobox C13) This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, which are located on different chromosomes and consist of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXC genes located in a cluster on chromosome 12. The product of this gene may play a role in the development of hair, nail, and filiform papilla. [provided by RefSeq, Jul 2008]

HOXC13 links:

HOXC13-AS (HGNC:):

HOXC13-AS links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_017410.3. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant 12-53938949-C-CTTA is Benign according to our data. Variant chr12-53938949-C-CTTA is described in ClinVar as [Benign]. Clinvar id is 2033340.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.068 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HOXC13	NM_017410.3 linkuse as main transcript	c.45_47dupTAT	p.Leu15_Met16insIle	disruptive_inframe_insertion	1/2	ENST00000243056.5	NP_059106.2	P31276
HOXC13-AS	NR_047507.1 linkuse as main transcript	n.173+519_173+521dupTAA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HOXC13	ENST00000243056.5 linkuse as main transcript	c.45_47dupTAT	p.Leu15_Met16insIle	disruptive_inframe_insertion	1/2	1	NM_017410.3	ENSP00000243056.3		P31276
HOXC13-AS	ENST00000512916.2 linkuse as main transcript	n.173+519_173+521dupTAA		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0157

AC:

2387

AN:

152210

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00311

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.0124

Gnomad ASJ

AF:

0.0176

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0740

Gnomad FIN

AF:

0.0138

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0209

Gnomad OTH

AF:

0.0205

GnomAD3 exomes

AF:

0.0219

AC:

3780

AN:

172822

Hom.:

108

AF XY:

0.0259

AC XY:

2488

AN XY:

95896

show subpopulations

Gnomad AFR exome

AF:

0.00402

Gnomad AMR exome

AF:

0.00722

Gnomad ASJ exome

AF:

0.0166

Gnomad EAS exome

AF:

0.000238

Gnomad SAS exome

AF:

0.0736

Gnomad FIN exome

AF:

0.0106

Gnomad NFE exome

AF:

0.0176

Gnomad OTH exome

AF:

0.0247

GnomAD4 exome

AF:

0.0214

AC:

30039

AN:

1406320

Hom.:

572

Cov.:

AF XY:

0.0231

AC XY:

16106

AN XY:

697224

show subpopulations

Gnomad4 AFR exome

AF:

0.00312

Gnomad4 AMR exome

AF:

0.00858

Gnomad4 ASJ exome

AF:

0.0163

Gnomad4 EAS exome

AF:

0.0000554

Gnomad4 SAS exome

AF:

0.0764

Gnomad4 FIN exome

AF:

0.0129

Gnomad4 NFE exome

AF:

0.0191

Gnomad4 OTH exome

AF:

0.0220

GnomAD4 genome

AF:

0.0157

AC:

2388

AN:

152322

Hom.:

Cov.:

AF XY:

0.0163

AC XY:

1214

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.00310

Gnomad4 AMR

AF:

0.0124

Gnomad4 ASJ

AF:

0.0176

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0743

Gnomad4 FIN

AF:

0.0138

Gnomad4 NFE

AF:

0.0209

Gnomad4 OTH

AF:

0.0203

Alfa

AF:

0.0182

Hom.:

Bravo

AF:

0.0132

Asia WGS

AF:

0.0220

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 25, 2024

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over