chr22-43833672-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_014351.4(SULT4A1):c.571G>A(p.Val191Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000201 in 1,595,430 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 (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000019 ( 0 hom. )
Consequence
SULT4A1
NM_014351.4 missense
NM_014351.4 missense
Scores
9
10
Clinical Significance
Conservation
PhyloP100: 3.28
Genes affected
SULT4A1 (HGNC:14903): (sulfotransferase family 4A member 1) This gene encodes a member of the sulfotransferase family. The encoded protein is a brain-specific sulfotransferase believed to be involved in the metabolism of neurotransmitters. Polymorphisms in this gene may be associated with susceptibility to schizophrenia. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.3504877).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SULT4A1 | NM_014351.4 | c.571G>A | p.Val191Met | missense_variant | 5/7 | ENST00000330884.9 | |
SULT4A1 | XM_047441321.1 | c.571G>A | p.Val191Met | missense_variant | 5/7 | ||
SULT4A1 | XM_011530121.2 | c.232G>A | p.Val78Met | missense_variant | 2/4 | ||
SULT4A1 | XM_047441322.1 | c.232G>A | p.Val78Met | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SULT4A1 | ENST00000330884.9 | c.571G>A | p.Val191Met | missense_variant | 5/7 | 1 | NM_014351.4 | P1 | |
SULT4A1 | ENST00000422525.1 | c.571G>A | p.Val191Met | missense_variant, NMD_transcript_variant | 5/8 | 1 | |||
SULT4A1 | ENST00000475131.1 | n.110G>A | non_coding_transcript_exon_variant | 2/3 | 4 | ||||
SULT4A1 | ENST00000432404.5 | c.*212G>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152198Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000181 AC: 4AN: 220488Hom.: 0 AF XY: 0.0000168 AC XY: 2AN XY: 118740
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GnomAD4 exome AF: 0.0000194 AC: 28AN: 1443114Hom.: 0 Cov.: 32 AF XY: 0.0000168 AC XY: 12AN XY: 715980
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GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74478
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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 | Nov 16, 2022 | The c.571G>A (p.V191M) alteration is located in exon 5 (coding exon 5) of the SULT4A1 gene. This alteration results from a G to A substitution at nucleotide position 571, causing the valine (V) at amino acid position 191 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
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Uncertain
D
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Uncertain
T
MutationAssessor
Benign
L
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
P
Vest4
MutPred
Gain of sheet (P = 0.1945);
MVP
MPC
ClinPred
T
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