rs76451666
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032495.6(HOPX):c.199-1886G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0613 in 1,550,766 control chromosomes in the GnomAD database, including 3,351 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 0.047 ( 254 hom., cov: 32)
Exomes 𝑓: 0.063 ( 3097 hom. )
Consequence
HOPX
NM_032495.6 intron
NM_032495.6 intron
Scores
14
Splicing: ADA: 0.7131
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.02
Genes affected
HOPX (HGNC:24961): (HOP homeobox) The protein encoded by this gene is a homeodomain protein that lacks certain conserved residues required for DNA binding. It was reported that choriocarcinoma cell lines and tissues failed to express this gene, which suggested the possible involvement of this gene in malignant conversion of placental trophoblasts. Studies in mice suggest that this protein may interact with serum response factor (SRF) and modulate SRF-dependent cardiac-specific gene expression and cardiac development. Multiple alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Feb 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0015913248).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0703 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOPX | NM_032495.6 | c.199-1886G>A | intron_variant | ENST00000420433.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOPX | ENST00000420433.6 | c.199-1886G>A | intron_variant | 5 | NM_032495.6 |
Frequencies
GnomAD3 genomes ? AF: 0.0474 AC: 7213AN: 152130Hom.: 255 Cov.: 32
GnomAD3 genomes
?
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7213
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152130
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32
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GnomAD3 exomes AF: 0.0470 AC: 7400AN: 157336Hom.: 231 AF XY: 0.0465 AC XY: 3864AN XY: 83156
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GnomAD4 exome AF: 0.0628 AC: 87823AN: 1398518Hom.: 3097 Cov.: 30 AF XY: 0.0619 AC XY: 42713AN XY: 689826
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GnomAD4 genome ? AF: 0.0474 AC: 7209AN: 152248Hom.: 254 Cov.: 32 AF XY: 0.0454 AC XY: 3380AN XY: 74438
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7209
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272
ALSPAC
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247
ExAC
?
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963
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27
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Vest4
MPC
ClinPred
T
GERP RS
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at