chr7-27156494-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_006896.4(HOXA7):ā€‹c.52G>Cā€‹(p.Ala18Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A18T) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 35)
Exomes š‘“: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

HOXA7
NM_006896.4 missense

Scores

1
7
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.44
Variant links:
Genes affected
HOXA7 (HGNC:5108): (homeobox A7) In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. For example, the encoded protein represses the transcription of differentiation-specific genes during keratinocyte proliferation, but this repression is then overcome by differentiation signals. This gene is highly similar to the antennapedia (Antp) gene of Drosophila. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HOXA7NM_006896.4 linkuse as main transcriptc.52G>C p.Ala18Pro missense_variant 1/2 ENST00000242159.5 NP_008827.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HOXA7ENST00000242159.5 linkuse as main transcriptc.52G>C p.Ala18Pro missense_variant 1/21 NM_006896.4 ENSP00000242159 P1
HOXA7ENST00000519842.1 linkuse as main transcriptc.52G>C p.Ala18Pro missense_variant 3/33 ENSP00000428563

Frequencies

GnomAD3 genomes
Cov.:
35
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1444610
Hom.:
0
Cov.:
43
AF XY:
0.00
AC XY:
0
AN XY:
716234
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
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.:
35

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.25
BayesDel_addAF
Uncertain
0.022
T
BayesDel_noAF
Benign
-0.21
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.11
T;.
Eigen
Uncertain
0.39
Eigen_PC
Uncertain
0.39
FATHMM_MKL
Pathogenic
1.0
D
LIST_S2
Benign
0.80
T;T
M_CAP
Benign
0.060
D
MetaRNN
Uncertain
0.67
D;D
MetaSVM
Benign
-0.30
T
MutationAssessor
Benign
1.7
L;.
MutationTaster
Benign
0.0047
P
PrimateAI
Uncertain
0.58
T
PROVEAN
Benign
-0.83
N;D
REVEL
Benign
0.15
Sift
Uncertain
0.029
D;.
Sift4G
Benign
0.13
T;.
Polyphen
0.99
D;.
Vest4
0.67
MutPred
0.43
Gain of disorder (P = 0.0505);Gain of disorder (P = 0.0505);
MVP
0.79
MPC
0.88
ClinPred
0.84
D
GERP RS
4.3
Varity_R
0.26
gMVP
0.66

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: rs2301721; hg19: chr7-27196113; API