4-69857541-G-C
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_005420.3(SULT1E1):āc.104C>Gā(p.Ala35Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000129 in 1,612,860 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 (ā ).
Frequency
Genomes: š 0.000046 ( 0 hom., cov: 32)
Exomes š: 0.00014 ( 0 hom. )
Consequence
SULT1E1
NM_005420.3 missense
NM_005420.3 missense
Scores
9
10
Clinical Significance
Conservation
PhyloP100: 1.67
Genes affected
SULT1E1 (HGNC:11377): (sulfotransferase family 1E 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 a protein that transfers a sulfo moiety to and from estrone, which may control levels of estrogen receptors. [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=0.31656283).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SULT1E1 | NM_005420.3 | c.104C>G | p.Ala35Gly | missense_variant | 2/8 | ENST00000226444.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SULT1E1 | ENST00000226444.4 | c.104C>G | p.Ala35Gly | missense_variant | 2/8 | 1 | NM_005420.3 | P1 | |
SULT1E1 | ENST00000504002.1 | n.210C>G | non_coding_transcript_exon_variant | 2/5 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152080Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000599 AC: 15AN: 250288Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135310
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GnomAD4 exome AF: 0.000138 AC: 201AN: 1460780Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 88AN XY: 726682
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GnomAD4 genome AF: 0.0000460 AC: 7AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74292
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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 | Aug 02, 2021 | The c.104C>G (p.A35G) alteration is located in exon 2 (coding exon 1) of the SULT1E1 gene. This alteration results from a C to G substitution at nucleotide position 104, causing the alanine (A) at amino acid position 35 to be replaced by a glycine (G). 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
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
P
Vest4
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