16-28608813-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001055.4(SULT1A1):c.43G>A(p.Val15Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 151,992 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 36)
Exomes 𝑓: 0.000018 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SULT1A1
NM_001055.4 missense
NM_001055.4 missense
Scores
2
6
9
Clinical Significance
Conservation
PhyloP100: -0.0800
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.43G>A | p.Val15Met | missense_variant | 2/8 | ENST00000314752.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SULT1A1 | ENST00000314752.12 | c.43G>A | p.Val15Met | missense_variant | 2/8 | 1 | NM_001055.4 | P1 | |
SULT1A1 | ENST00000569554.5 | c.43G>A | p.Val15Met | missense_variant | 1/7 | 1 | P1 | ||
SULT1A1 | ENST00000566189.5 | c.43G>A | p.Val15Met | missense_variant | 2/8 | 5 | |||
SULT1A1 | ENST00000567512.1 | c.43G>A | p.Val15Met | missense_variant | 2/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151992Hom.: 0 Cov.: 36
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?
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GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250392Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135520
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000185 AC: 27AN: 1459840Hom.: 0 Cov.: 36 AF XY: 0.0000179 AC XY: 13AN XY: 726228
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151992Hom.: 0 Cov.: 36 AF XY: 0.0000135 AC XY: 1AN XY: 74238
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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 15, 2023 | The c.43G>A (p.V15M) alteration is located in exon 2 (coding exon 1) of the SULT1A1 gene. This alteration results from a G to A substitution at nucleotide position 43, causing the valine (V) at amino acid position 15 to be replaced by a methionine (M). 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
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Uncertain
T;T;T;T;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
M_CAP
Benign
T
MetaRNN
Uncertain
T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;M;M;M;.;.
MutationTaster
Benign
D;N;N;N;N
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
N;N;N;N;N;N
Sift
Uncertain
D;D;D;D;D;D
Sift4G
Uncertain
D;D;D;D;.;.
Polyphen
D;D;D;D;.;.
Vest4
MutPred
Loss of methylation at K16 (P = 0.0251);Loss of methylation at K16 (P = 0.0251);Loss of methylation at K16 (P = 0.0251);Loss of methylation at K16 (P = 0.0251);Loss of methylation at K16 (P = 0.0251);Loss of methylation at K16 (P = 0.0251);
MVP
MPC
2.6
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