chr20-45512812-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006652.2(SPINT3):c.109G>A(p.Ala37Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000245 in 1,551,598 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006652.2 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPINT3 | NM_006652.2 | c.109G>A | p.Ala37Thr | missense_variant | 2/2 | ENST00000217428.7 | |
LOC107987282 | XR_001754641.3 | n.100-20462C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPINT3 | ENST00000217428.7 | c.109G>A | p.Ala37Thr | missense_variant | 2/2 | 1 | NM_006652.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000703 AC: 11AN: 156420Hom.: 0 AF XY: 0.0000724 AC XY: 6AN XY: 82820
GnomAD4 exome AF: 0.0000214 AC: 30AN: 1399326Hom.: 0 Cov.: 33 AF XY: 0.0000203 AC XY: 14AN XY: 690162
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 22, 2023 | The c.109G>A (p.A37T) alteration is located in exon 2 (coding exon 2) of the SPINT3 gene. This alteration results from a G to A substitution at nucleotide position 109, causing the alanine (A) at amino acid position 37 to be replaced by a threonine (T). 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