rs3832095
Your query was ambiguous. Multiple possible variants found:
- chr2-176093057-GGGCGGCGGCGGC-G
- chr2-176093057-GGGCGGCGGCGGC-GGGC
- chr2-176093057-GGGCGGCGGCGGC-GGGCGGC
- chr2-176093057-GGGCGGCGGCGGC-GGGCGGCGGC
- chr2-176093057-GGGCGGCGGCGGC-GGGCGGCGGCGGCGGC
- chr2-176093057-GGGCGGCGGCGGC-GGGCGGCGGCGGCGGCGGC
- chr2-176093057-GGGCGGCGGCGGC-GGGCGGCGGCGGCGGCGGCGGC
- chr2-176093057-GGGCGGCGGCGGC-GGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chr2-176093057-GGGCGGCGGCGGC-GGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chr2-176093057-GGGCGGCGGCGGC-GGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chr2-176093057-GGGCGGCGGCGGC-GGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chr2-176093057-GGGCGGCGGCGGC-GGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chr2-176093057-GGGCGGCGGCGGC-GGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chr2-176093057-GGGCGGCGGCGGC-GGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chr2-176093057-GGGCGGCGGCGGC-GGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chr2-176093057-GGGCGGCGGCGGC-GGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
Variant summary
Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2PM4
The NM_000523.4(HOXD13):c.174_182delGGCGGCGGC(p.Ala59_Ala61del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000219 in 1,369,814 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000016 ( 0 hom. )
Consequence
HOXD13
NM_000523.4 disruptive_inframe_deletion
NM_000523.4 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.39
Publications
1 publications found
Genes affected
HOXD13 (HGNC:5136): (homeobox D13) 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 in a cluster on chromosome 2. Deletions that remove the entire HOXD gene cluster or the 5' end of this cluster have been associated with severe limb and genital abnormalities. Mutations in this particular gene cause synpolydactyly. [provided by RefSeq, Jul 2008]
HOXD13 Gene-Disease associations (from GenCC):
- brachydactyly-syndactyly syndromeInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Laboratory for Molecular Medicine, G2P
- synpolydactyly type 1Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
- brachydactyly type EInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- syndactyly type 5Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_000523.4.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000523.4. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes 0.00000663 AC: 1AN: 150788Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
150788
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000164 AC: 2AN: 1219026Hom.: 0 AF XY: 0.00000168 AC XY: 1AN XY: 595810 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
2
AN:
1219026
Hom.:
AF XY:
AC XY:
1
AN XY:
595810
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
24022
American (AMR)
AF:
AC:
0
AN:
10562
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
16996
East Asian (EAS)
AF:
AC:
0
AN:
28024
South Asian (SAS)
AF:
AC:
0
AN:
50160
European-Finnish (FIN)
AF:
AC:
0
AN:
30800
Middle Eastern (MID)
AF:
AC:
0
AN:
4814
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1003626
Other (OTH)
AF:
AC:
1
AN:
50022
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0448430), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.350
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<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 0.00000663 AC: 1AN: 150788Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 73552 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
150788
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
73552
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41248
American (AMR)
AF:
AC:
0
AN:
15144
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3440
East Asian (EAS)
AF:
AC:
0
AN:
5130
South Asian (SAS)
AF:
AC:
0
AN:
4798
European-Finnish (FIN)
AF:
AC:
0
AN:
10298
Middle Eastern (MID)
AF:
AC:
0
AN:
310
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67450
Other (OTH)
AF:
AC:
0
AN:
2062
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.
Publications
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