rs570351507

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_006897.3(HOXC9):ā€‹c.497C>Gā€‹(p.Ala166Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000707 in 1,414,592 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes š‘“: 7.1e-7 ( 0 hom. )

Consequence

HOXC9
NM_006897.3 missense

Scores

5
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.97
Variant links:
Genes affected
HOXC9 (HGNC:5130): (homeobox C9) 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. [provided by RefSeq, Jul 2008]
HOXC6 (HGNC:5128): (homeobox C6) This gene belongs to the homeobox family, members of which 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, HOXC6, is one of several HOXC genes located in a cluster on chromosome 12. Three genes, HOXC5, HOXC4 and HOXC6, share a 5' non-coding exon. Transcripts may include the shared exon spliced to the gene-specific exons, or they may include only the gene-specific exons. Alternatively spliced transcript variants encoding different isoforms have been identified for HOXC6. Transcript variant two includes the shared exon, and transcript variant one includes only gene-specific exons. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.165964).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HOXC9NM_006897.3 linkc.497C>G p.Ala166Gly missense_variant Exon 1 of 2 ENST00000303450.5 NP_008828.1 P31274A0A024RAZ6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HOXC9ENST00000303450.5 linkc.497C>G p.Ala166Gly missense_variant Exon 1 of 2 1 NM_006897.3 ENSP00000302836.4 P31274
ENSG00000273049ENST00000513209.1 linkc.166+14675C>G intron_variant Intron 1 of 1 3 ENSP00000476742.1 V9GYH0

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000533
AC:
1
AN:
187640
Hom.:
0
AF XY:
0.00000948
AC XY:
1
AN XY:
105430
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000792
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
7.07e-7
AC:
1
AN:
1414592
Hom.:
0
Cov.:
31
AF XY:
0.00000142
AC XY:
1
AN XY:
702176
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000273
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.080
BayesDel_addAF
Uncertain
0.029
T
BayesDel_noAF
Benign
-0.20
CADD
Benign
22
DANN
Uncertain
0.98
DEOGEN2
Benign
0.052
T;T
Eigen
Benign
-0.18
Eigen_PC
Benign
-0.018
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Benign
0.46
.;T
M_CAP
Benign
0.048
D
MetaRNN
Benign
0.17
T;T
MetaSVM
Uncertain
-0.051
T
MutationAssessor
Benign
0.55
N;N
PrimateAI
Uncertain
0.76
T
PROVEAN
Benign
-0.23
N;N
REVEL
Benign
0.20
Sift
Benign
0.20
T;T
Sift4G
Benign
0.31
T;T
Polyphen
0.0010
B;B
Vest4
0.14
MutPred
0.38
Gain of catalytic residue at K169 (P = 0.0398);Gain of catalytic residue at K169 (P = 0.0398);
MVP
0.98
MPC
0.99
ClinPred
0.20
T
GERP RS
4.2
Varity_R
0.12

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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.

Other links and lift over

dbSNP: rs570351507; hg19: chr12-54394469; API