1-53772486-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018087.5(NDC1):c.1804G>A(p.Val602Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000011 in 1,460,236 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 (★).
Frequency
Consequence
NM_018087.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NDC1 | NM_018087.5 | c.1804G>A | p.Val602Ile | missense_variant | Exon 17 of 18 | ENST00000371429.4 | NP_060557.3 | |
NDC1 | NM_001168551.2 | c.1684G>A | p.Val562Ile | missense_variant | Exon 17 of 18 | NP_001162023.1 | ||
NDC1 | XM_011541766.3 | c.1801G>A | p.Val601Ile | missense_variant | Exon 17 of 18 | XP_011540068.1 | ||
NDC1 | NR_033142.2 | n.1718G>A | non_coding_transcript_exon_variant | Exon 16 of 17 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250894Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135606
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1460236Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 726480
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1804G>A (p.V602I) alteration is located in exon 17 (coding exon 17) of the NDC1 gene. This alteration results from a G to A substitution at nucleotide position 1804, causing the valine (V) at amino acid position 602 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