Variant 2-176150242-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000432796.2(HOXD3):c.-85+13243G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 493,164 control chromosomes in the GnomAD database, including 41,966 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 0.30 ( 8733 hom., cov: 32)

Exomes 𝑓: 0.42 ( 33233 hom. )

Consequence

HOXD3
ENST00000432796.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.807

Variant links:

Genes affected

HOXD3 (HGNC:5137): (homeobox D3) 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, located on different chromosomes, consisting of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXD genes located at 2q31-2q37 chromosome regions. Deletions that removed the entire HOXD gene cluster or 5' end of this cluster have been associated with severe limb and genital abnormalities. The protein encoded by this gene may play a role in the regulation of cell adhesion processes. [provided by RefSeq, Jul 2008]

HOXD3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HOXD3	ENST00000432796.2 linkuse as main transcript	c.-85+13243G>T		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.302

AC:

45927

AN:

151936

Hom.:

8720

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0990

Gnomad AMI

AF:

0.385

Gnomad AMR

AF:

0.465

Gnomad ASJ

AF:

0.239

Gnomad EAS

AF:

0.628

Gnomad SAS

AF:

0.593

Gnomad FIN

AF:

0.402

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.331

Gnomad OTH

AF:

0.310

GnomAD4 exome

AF:

0.415

AC:

141675

AN:

341112

Hom.:

33233

AF XY:

0.428

AC XY:

82234

AN XY:

192320

show subpopulations

Gnomad4 AFR exome

AF:

0.0982

Gnomad4 AMR exome

AF:

0.638

Gnomad4 ASJ exome

AF:

0.241

Gnomad4 EAS exome

AF:

0.645

Gnomad4 SAS exome

AF:

0.585

Gnomad4 FIN exome

AF:

0.391

Gnomad4 NFE exome

AF:

0.330

Gnomad4 OTH exome

AF:

0.362

GnomAD4 genome

AF:

0.302

AC:

45942

AN:

152052

Hom.:

8733

Cov.:

AF XY:

0.315

AC XY:

23383

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.0987

Gnomad4 AMR

AF:

0.466

Gnomad4 ASJ

AF:

0.239

Gnomad4 EAS

AF:

0.628

Gnomad4 SAS

AF:

0.593

Gnomad4 FIN

AF:

0.402

Gnomad4 NFE

AF:

0.331

Gnomad4 OTH

AF:

0.310

Alfa

AF:

0.321

Hom.:

1142

Bravo

AF:

0.296

Asia WGS

AF:

0.566

AC:

1970

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

DANN

Benign

0.83

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