chr9-96465728-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014282.4(HABP4):c.693C>A(p.Asp231Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000356 in 1,602,758 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014282.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HABP4 | NM_014282.4 | c.693C>A | p.Asp231Glu | missense_variant | 4/8 | ENST00000375249.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HABP4 | ENST00000375249.5 | c.693C>A | p.Asp231Glu | missense_variant | 4/8 | 1 | NM_014282.4 | P1 | |
HABP4 | ENST00000375251.7 | c.512+7187C>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251454Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135904
GnomAD4 exome AF: 0.0000172 AC: 25AN: 1450620Hom.: 0 Cov.: 27 AF XY: 0.0000125 AC XY: 9AN XY: 722450
GnomAD4 genome AF: 0.000210 AC: 32AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 23, 2023 | The c.693C>A (p.D231E) alteration is located in exon 4 (coding exon 4) of the HABP4 gene. This alteration results from a C to A substitution at nucleotide position 693, causing the aspartic acid (D) at amino acid position 231 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at