chr19-45152540-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198478.4(NKPD1):c.1897G>T(p.Val633Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000014 in 1,428,622 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198478.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NKPD1 | NM_198478.4 | c.1897G>T | p.Val633Leu | missense_variant | 5/5 | ENST00000686631.1 | |
NKPD1 | XM_011526799.3 | c.1978G>T | p.Val660Leu | missense_variant | 5/5 | ||
NKPD1 | XM_011526804.3 | c.1540G>T | p.Val514Leu | missense_variant | 4/4 | ||
NKPD1 | XM_011526805.3 | c.1372G>T | p.Val458Leu | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NKPD1 | ENST00000686631.1 | c.1897G>T | p.Val633Leu | missense_variant | 5/5 | NM_198478.4 | P2 | ||
NKPD1 | ENST00000317951.6 | c.1897G>T | p.Val633Leu | missense_variant | 5/5 | 2 | P2 | ||
NKPD1 | ENST00000589776.1 | c.1231G>T | p.Val411Leu | missense_variant | 1/1 | A2 | |||
MARK4 | ENST00000587566.5 | c.-277+73163C>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000140 AC: 2AN: 1428622Hom.: 0 Cov.: 32 AF XY: 0.00000141 AC XY: 1AN XY: 710252
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 21, 2023 | The c.1897G>T (p.V633L) alteration is located in exon 4 (coding exon 4) of the NKPD1 gene. This alteration results from a G to T substitution at nucleotide position 1897, causing the valine (V) at amino acid position 633 to be replaced by a leucine (L). 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