20-45723925-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_178455.3(SPINT4):c.161A>C(p.His54Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,450,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178455.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPINT4 | NM_178455.3 | c.161A>C | p.His54Pro | missense_variant | Exon 2 of 3 | ENST00000279058.4 | NP_848550.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000416 AC: 1AN: 240262Hom.: 0 AF XY: 0.00000770 AC XY: 1AN XY: 129918
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1450872Hom.: 0 Cov.: 30 AF XY: 0.00000277 AC XY: 2AN XY: 721682
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.161A>C (p.H54P) alteration is located in exon 2 (coding exon 2) of the SPINT4 gene. This alteration results from a A to C substitution at nucleotide position 161, causing the histidine (H) at amino acid position 54 to be replaced by a proline (P). 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