17-81559372-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017921.4(NPLOC4):c.1714G>A(p.Val572Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000994 in 1,609,332 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017921.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NPLOC4 | NM_017921.4 | c.1714G>A | p.Val572Ile | missense_variant | Exon 17 of 17 | ENST00000331134.11 | NP_060391.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000423 AC: 1AN: 236566Hom.: 0 AF XY: 0.00000775 AC XY: 1AN XY: 129038
GnomAD4 exome AF: 0.00000961 AC: 14AN: 1457132Hom.: 0 Cov.: 30 AF XY: 0.00000828 AC XY: 6AN XY: 724426
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1714G>A (p.V572I) alteration is located in exon 17 (coding exon 17) of the NPLOC4 gene. This alteration results from a G to A substitution at nucleotide position 1714, causing the valine (V) at amino acid position 572 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