chr8-75560353-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004133.5(HNF4G):c.1133A>G(p.Asn378Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000465 in 1,613,140 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004133.5 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 |
---|---|---|---|---|---|---|---|
HNF4G | NM_004133.5 | c.1133A>G | p.Asn378Ser | missense_variant | 9/10 | ENST00000396423.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HNF4G | ENST00000396423.4 | c.1133A>G | p.Asn378Ser | missense_variant | 9/10 | 1 | NM_004133.5 | ||
HNF4G | ENST00000354370.5 | c.992A>G | p.Asn331Ser | missense_variant | 10/11 | 1 | P1 | ||
HNF4G | ENST00000674002.1 | c.1103A>G | p.Asn368Ser | missense_variant | 9/10 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250738Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135478
GnomAD4 exome AF: 0.0000431 AC: 63AN: 1460928Hom.: 0 Cov.: 31 AF XY: 0.0000427 AC XY: 31AN XY: 726792
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2022 | The c.1103A>G (p.N368S) alteration is located in exon 9 (coding exon 9) of the HNF4G gene. This alteration results from a A to G substitution at nucleotide position 1103, causing the asparagine (N) at amino acid position 368 to be replaced by a serine (S). 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