7-22492596-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001382447.1(STEAP1B):c.731C>A(p.Ser244Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00000435 in 1,608,292 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
STEAP1B
NM_001382447.1 missense
NM_001382447.1 missense
Scores
12
7
Clinical Significance
Conservation
PhyloP100: 4.43
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STEAP1B | NM_001382447.1 | c.731C>A | p.Ser244Tyr | missense_variant | 4/5 | ENST00000678116.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STEAP1B | ENST00000678116.1 | c.731C>A | p.Ser244Tyr | missense_variant | 4/5 | NM_001382447.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152056Hom.: 0 Cov.: 30
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GnomAD4 exome AF: 0.00000206 AC: 3AN: 1456236Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 724130
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GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152056Hom.: 0 Cov.: 30 AF XY: 0.0000269 AC XY: 2AN XY: 74254
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 26, 2023 | The c.731C>A (p.S244Y) alteration is located in exon 4 (coding exon 3) of the STEAP1B gene. This alteration results from a C to A substitution at nucleotide position 731, causing the serine (S) at amino acid position 244 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Uncertain
D;.;D
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;.;.
MutationTaster
Benign
N;N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D
REVEL
Uncertain
Sift
Uncertain
D;D;D
Sift4G
Uncertain
D;D;D
Polyphen
D;.;.
Vest4
MutPred
Loss of disorder (P = 0.0127);.;.;
MVP
MPC
3.4
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at