16-1256309-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_012217.3(TPSD1):c.29G>A(p.Ser10Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,613,266 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012217.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TPSD1 | ENST00000211076.5 | c.29G>A | p.Ser10Asn | missense_variant | 1/5 | 1 | NM_012217.3 | ENSP00000211076.3 | ||
TPSD1 | ENST00000397534.6 | c.8G>A | p.Ser3Asn | missense_variant | 2/6 | 5 | ENSP00000380668.2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152230Hom.: 0 Cov.: 40
GnomAD3 exomes AF: 0.0000400 AC: 10AN: 250280Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135496
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1460918Hom.: 0 Cov.: 70 AF XY: 0.0000440 AC XY: 32AN XY: 726822
GnomAD4 genome AF: 0.0000656 AC: 10AN: 152348Hom.: 0 Cov.: 40 AF XY: 0.0000537 AC XY: 4AN XY: 74504
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.29G>A (p.S10N) alteration is located in exon 1 (coding exon 1) of the TPSD1 gene. This alteration results from a G to A substitution at nucleotide position 29, causing the serine (S) at amino acid position 10 to be replaced by an asparagine (N). 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