rs10968457
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014878.5(PUM3):c.38G>A(p.Ser13Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0371 in 1,612,134 control chromosomes in the GnomAD database, including 1,282 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_014878.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PUM3 | NM_014878.5 | c.38G>A | p.Ser13Asn | missense_variant | 2/18 | ENST00000397885.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PUM3 | ENST00000397885.3 | c.38G>A | p.Ser13Asn | missense_variant | 2/18 | 1 | NM_014878.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0350 AC: 5328AN: 152096Hom.: 104 Cov.: 32
GnomAD3 exomes AF: 0.0404 AC: 10060AN: 249140Hom.: 225 AF XY: 0.0398 AC XY: 5378AN XY: 135186
GnomAD4 exome AF: 0.0373 AC: 54476AN: 1459920Hom.: 1178 Cov.: 30 AF XY: 0.0374 AC XY: 27133AN XY: 726382
GnomAD4 genome ? AF: 0.0350 AC: 5333AN: 152214Hom.: 104 Cov.: 32 AF XY: 0.0343 AC XY: 2554AN XY: 74420
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at