19-40441953-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_203344.3(SERTAD3):c.128G>A(p.Arg43His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00027 in 1,570,360 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R43S) has been classified as Uncertain significance.
Frequency
Consequence
NM_203344.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SERTAD3 | NM_203344.3 | c.128G>A | p.Arg43His | missense_variant | Exon 2 of 2 | ENST00000322354.4 | NP_976219.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SERTAD3 | ENST00000322354.4 | c.128G>A | p.Arg43His | missense_variant | Exon 2 of 2 | 1 | NM_203344.3 | ENSP00000325414.2 | ||
SERTAD3 | ENST00000392028.8 | c.128G>A | p.Arg43His | missense_variant | Exon 2 of 2 | 1 | ENSP00000375882.3 | |||
SERTAD3 | ENST00000599706.1 | c.128G>A | p.Arg43His | missense_variant | Exon 2 of 2 | 2 | ENSP00000469245.1 | |||
SERTAD3 | ENST00000596456.1 | c.128G>A | p.Arg43His | missense_variant | Exon 3 of 3 | 3 | ENSP00000472999.1 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 22AN: 210720Hom.: 0 AF XY: 0.000133 AC XY: 15AN XY: 113050
GnomAD4 exome AF: 0.000276 AC: 391AN: 1418164Hom.: 0 Cov.: 32 AF XY: 0.000292 AC XY: 205AN XY: 701816
GnomAD4 genome AF: 0.000217 AC: 33AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.000256 AC XY: 19AN XY: 74340
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at