chr14-23276054-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020834.3(HOMEZ):c.1174A>G(p.Ile392Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,613,974 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020834.3 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 |
---|---|---|---|---|---|---|---|
HOMEZ | NM_020834.3 | c.1174A>G | p.Ile392Val | missense_variant | 2/2 | ENST00000357460.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOMEZ | ENST00000357460.7 | c.1174A>G | p.Ile392Val | missense_variant | 2/2 | 1 | NM_020834.3 | P2 | |
HOMEZ | ENST00000561013.3 | c.1180A>G | p.Ile394Val | missense_variant | 3/3 | 2 | A2 | ||
HOMEZ | ENST00000673724.1 | c.841A>G | p.Ile281Val | missense_variant | 3/3 | A2 | |||
HOMEZ | ENST00000606731.2 | c.664A>G | p.Ile222Val | missense_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000924 AC: 23AN: 249034Hom.: 0 AF XY: 0.0000888 AC XY: 12AN XY: 135112
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461658Hom.: 0 Cov.: 36 AF XY: 0.0000248 AC XY: 18AN XY: 727106
GnomAD4 genome ? AF: 0.0000919 AC: 14AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 25, 2023 | The c.1174A>G (p.I392V) alteration is located in exon 2 (coding exon 2) of the HOMEZ gene. This alteration results from a A to G substitution at nucleotide position 1174, causing the isoleucine (I) at amino acid position 392 to be replaced by a valine (V). 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