chr16-28608800-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001055.4(SULT1A1):c.56C>A(p.Pro19Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000526 in 151,972 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 36)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SULT1A1
NM_001055.4 missense
NM_001055.4 missense
Scores
4
5
8
Clinical Significance
Conservation
PhyloP100: 2.70
Genes affected
SULT1A1 (HGNC:11453): (sulfotransferase family 1A member 1) Sulfotransferase enzymes catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs, and xenobiotic compounds. These cytosolic enzymes are different in their tissue distributions and substrate specificities. The gene structure (number and length of exons) is similar among family members. This gene encodes one of two phenol sulfotransferases with thermostable enzyme activity. Multiple alternatively spliced variants that encode two isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
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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 |
---|---|---|---|---|---|---|---|
SULT1A1 | NM_001055.4 | c.56C>A | p.Pro19Gln | missense_variant | 2/8 | ENST00000314752.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SULT1A1 | ENST00000314752.12 | c.56C>A | p.Pro19Gln | missense_variant | 2/8 | 1 | NM_001055.4 | P1 | |
SULT1A1 | ENST00000569554.5 | c.56C>A | p.Pro19Gln | missense_variant | 1/7 | 1 | P1 | ||
SULT1A1 | ENST00000566189.5 | c.56C>A | p.Pro19Gln | missense_variant | 2/8 | 5 | |||
SULT1A1 | ENST00000567512.1 | c.56C>A | p.Pro19Gln | missense_variant | 2/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 151972Hom.: 0 Cov.: 36
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?
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GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250254Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135450
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000411 AC: 6AN: 1459984Hom.: 0 Cov.: 36 AF XY: 0.00000688 AC XY: 5AN XY: 726284
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 151972Hom.: 0 Cov.: 36 AF XY: 0.0000539 AC XY: 4AN XY: 74222
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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 | Mar 01, 2024 | The c.56C>A (p.P19Q) alteration is located in exon 2 (coding exon 1) of the SULT1A1 gene. This alteration results from a C to A substitution at nucleotide position 56, causing the proline (P) at amino acid position 19 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Uncertain
D;D;D;D;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Benign
T
MetaRNN
Uncertain
T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;M;M;M;.;.
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;D;D;D;D;D
Sift
Uncertain
D;D;D;D;D;D
Sift4G
Benign
T;T;T;T;.;.
Polyphen
D;D;D;D;.;.
Vest4
MVP
MPC
3.0
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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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