chr19-48591686-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS1
The NM_177973.2(SULT2B1):c.501G>A(p.Lys167=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00264 in 1,613,044 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0019 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0027 ( 7 hom. )
Consequence
SULT2B1
NM_177973.2 synonymous
NM_177973.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.384
Genes affected
SULT2B1 (HGNC:11459): (sulfotransferase family 2B 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 sulfates dehydroepiandrosterone but not 4-nitrophenol, a typical substrate for the phenol and estrogen sulfotransferase subfamilies. Two alternatively spliced variants that encode different isoforms have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
?
Variant 19-48591686-G-A is Benign according to our data. Variant chr19-48591686-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 720878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.384 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00189 (287/152202) while in subpopulation NFE AF= 0.00287 (195/68004). AF 95% confidence interval is 0.00254. There are 0 homozygotes in gnomad4. There are 136 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SULT2B1 | NM_177973.2 | c.501G>A | p.Lys167= | synonymous_variant | 4/7 | ENST00000201586.7 | |
SULT2B1 | NM_004605.2 | c.456G>A | p.Lys152= | synonymous_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SULT2B1 | ENST00000201586.7 | c.501G>A | p.Lys167= | synonymous_variant | 4/7 | 1 | NM_177973.2 | P2 | |
SULT2B1 | ENST00000323090.4 | c.456G>A | p.Lys152= | synonymous_variant | 3/6 | 1 | A2 | ||
ENST00000666424.1 | n.493+5060C>T | intron_variant, non_coding_transcript_variant | |||||||
SULT2B1 | ENST00000594274.1 | n.251G>A | non_coding_transcript_exon_variant | 2/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00189 AC: 287AN: 152084Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00191 AC: 476AN: 249484Hom.: 0 AF XY: 0.00201 AC XY: 271AN XY: 134892
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GnomAD4 exome AF: 0.00272 AC: 3977AN: 1460842Hom.: 7 Cov.: 31 AF XY: 0.00270 AC XY: 1962AN XY: 726656
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
SULT2B1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 11, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 07, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at