chr1-53772359-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018087.5(NDC1):c.1931G>A(p.Arg644Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000205 in 1,613,522 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NDC1 | NM_018087.5 | c.1931G>A | p.Arg644Gln | missense_variant | Exon 17 of 18 | ENST00000371429.4 | NP_060557.3 | |
NDC1 | NM_001168551.2 | c.1811G>A | p.Arg604Gln | missense_variant | Exon 17 of 18 | NP_001162023.1 | ||
NDC1 | XM_011541766.3 | c.1928G>A | p.Arg643Gln | missense_variant | Exon 17 of 18 | XP_011540068.1 | ||
NDC1 | NR_033142.2 | n.1845G>A | non_coding_transcript_exon_variant | Exon 16 of 17 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152054Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251282Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135798
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461468Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 727070
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152054Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74260
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1931G>A (p.R644Q) 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 1931, causing the arginine (R) at amino acid position 644 to be replaced by a glutamine (Q). 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