chr21-42903533-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021075.4(NDUFV3):c.521C>T(p.Thr174Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000892 in 1,614,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021075.4 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 |
---|---|---|---|---|---|---|---|
NDUFV3 | NM_021075.4 | c.521C>T | p.Thr174Ile | missense_variant | 3/4 | ENST00000354250.7 | |
NDUFV3 | XM_011529586.3 | c.521C>T | p.Thr174Ile | missense_variant | 3/5 | ||
NDUFV3 | NM_001001503.2 | c.170-5331C>T | intron_variant | ||||
NDUFV3 | XM_017028359.2 | c.170-3307C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDUFV3 | ENST00000354250.7 | c.521C>T | p.Thr174Ile | missense_variant | 3/4 | 1 | NM_021075.4 | ||
NDUFV3 | ENST00000340344.4 | c.170-5331C>T | intron_variant | 1 | P1 | ||||
NDUFV3 | ENST00000460259.1 | n.1044C>T | non_coding_transcript_exon_variant | 5/6 | 2 | ||||
NDUFV3 | ENST00000460740.1 | n.413C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 251036Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135764
GnomAD4 exome AF: 0.0000903 AC: 132AN: 1461840Hom.: 0 Cov.: 76 AF XY: 0.0000825 AC XY: 60AN XY: 727228
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 24, 2023 | The c.521C>T (p.T174I) alteration is located in exon 3 (coding exon 3) of the NDUFV3 gene. This alteration results from a C to T substitution at nucleotide position 521, causing the threonine (T) at amino acid position 174 to be replaced by an isoleucine (I). 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