2-191685667-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001031716.5(NABP1):c.514C>T(p.Arg172Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,768 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001031716.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NABP1 | NM_001031716.5 | c.514C>T | p.Arg172Trp | missense_variant | Exon 6 of 6 | ENST00000425611.9 | NP_001026886.1 | |
NABP1 | NM_001254736.3 | c.274C>T | p.Arg92Trp | missense_variant | Exon 6 of 6 | NP_001241665.1 | ||
NABP1 | NR_045622.3 | n.633C>T | non_coding_transcript_exon_variant | Exon 7 of 7 | ||||
NABP1 | NR_045623.3 | n.1097C>T | non_coding_transcript_exon_variant | Exon 7 of 7 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152052Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251184Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135760
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461716Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727156
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152052Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74278
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.514C>T (p.R172W) alteration is located in exon 6 (coding exon 6) of the NABP1 gene. This alteration results from a C to T substitution at nucleotide position 514, causing the arginine (R) at amino acid position 172 to be replaced by a tryptophan (W). 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