chr21-42903486-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_021075.4(NDUFV3):c.474C>A(p.Ser158Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,200 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S158S) has been classified as Likely benign.
Frequency
Consequence
NM_021075.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDUFV3 | NM_021075.4 | c.474C>A | p.Ser158Arg | missense_variant | 3/4 | ENST00000354250.7 | |
NDUFV3 | XM_011529586.3 | c.474C>A | p.Ser158Arg | missense_variant | 3/5 | ||
NDUFV3 | NM_001001503.2 | c.170-5378C>A | intron_variant | ||||
NDUFV3 | XM_017028359.2 | c.170-3354C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDUFV3 | ENST00000354250.7 | c.474C>A | p.Ser158Arg | missense_variant | 3/4 | 1 | NM_021075.4 | ||
NDUFV3 | ENST00000340344.4 | c.170-5378C>A | intron_variant | 1 | P1 | ||||
NDUFV3 | ENST00000460259.1 | n.997C>A | non_coding_transcript_exon_variant | 5/6 | 2 | ||||
NDUFV3 | ENST00000460740.1 | n.366C>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 33
GnomAD4 exome Cov.: 76
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2024 | The c.474C>A (p.S158R) alteration is located in exon 3 (coding exon 3) of the NDUFV3 gene. This alteration results from a C to A substitution at nucleotide position 474, causing the serine (S) at amino acid position 158 to be replaced by an arginine (R). 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