2-119245747-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_182915.3(STEAP3):c.281C>T(p.Pro94Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,614,084 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P94P) has been classified as Benign.
Frequency
Consequence
NM_182915.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STEAP3 | NM_182915.3 | c.281C>T | p.Pro94Leu | missense_variant | 3/6 | ENST00000393110.7 | |
STEAP3-AS1 | NR_046721.1 | n.1893G>A | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STEAP3 | ENST00000393110.7 | c.281C>T | p.Pro94Leu | missense_variant | 3/6 | 1 | NM_182915.3 | ||
STEAP3-AS1 | ENST00000654197.1 | n.1295G>A | non_coding_transcript_exon_variant | 4/4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000123 AC: 31AN: 251132Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135756
GnomAD4 exome AF: 0.0000561 AC: 82AN: 1461874Hom.: 0 Cov.: 31 AF XY: 0.0000536 AC XY: 39AN XY: 727236
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 07, 2023 | The c.281C>T (p.P94L) alteration is located in exon 3 (coding exon 2) of the STEAP3 gene. This alteration results from a C to T substitution at nucleotide position 281, causing the proline (P) at amino acid position 94 to be replaced by a leucine (L). 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