chrX-44542000-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_173794.4(FUNDC1):c.130A>G(p.Met44Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000123 in 1,205,116 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 39 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173794.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FUNDC1 | NM_173794.4 | c.130A>G | p.Met44Val | missense_variant | 2/5 | ENST00000378045.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FUNDC1 | ENST00000378045.5 | c.130A>G | p.Met44Val | missense_variant | 2/5 | 1 | NM_173794.4 | P1 | |
FUNDC1 | ENST00000483115.1 | n.305A>G | non_coding_transcript_exon_variant | 1/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000170 AC: 19AN: 111451Hom.: 0 Cov.: 22 AF XY: 0.000149 AC XY: 5AN XY: 33633
GnomAD3 exomes AF: 0.000187 AC: 33AN: 176736Hom.: 0 AF XY: 0.000179 AC XY: 11AN XY: 61484
GnomAD4 exome AF: 0.000118 AC: 129AN: 1093665Hom.: 0 Cov.: 28 AF XY: 0.0000947 AC XY: 34AN XY: 359177
GnomAD4 genome ? AF: 0.000170 AC: 19AN: 111451Hom.: 0 Cov.: 22 AF XY: 0.000149 AC XY: 5AN XY: 33633
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 14, 2023 | The c.130A>G (p.M44V) alteration is located in exon 2 (coding exon 2) of the FUNDC1 gene. This alteration results from a A to G substitution at nucleotide position 130, causing the methionine (M) at amino acid position 44 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