chr20-45512803-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006652.2(SPINT3):c.118A>G(p.Met40Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000276 in 1,551,524 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.118A>G | p.Met40Val | missense_variant | 2/2 | ENST00000217428.7 | |
LOC107987282 | XR_001754641.3 | n.100-20471T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPINT3 | ENST00000217428.7 | c.118A>G | p.Met40Val | missense_variant | 2/2 | 1 | NM_006652.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000177 AC: 27AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000134 AC: 21AN: 156488Hom.: 0 AF XY: 0.000133 AC XY: 11AN XY: 82844
GnomAD4 exome AF: 0.000287 AC: 401AN: 1399376Hom.: 0 Cov.: 33 AF XY: 0.000259 AC XY: 179AN XY: 690184
GnomAD4 genome ? AF: 0.000177 AC: 27AN: 152148Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2022 | The c.118A>G (p.M40V) alteration is located in exon 2 (coding exon 2) of the SPINT3 gene. This alteration results from a A to G substitution at nucleotide position 118, causing the methionine (M) at amino acid position 40 to be replaced by a valine (V). 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