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GeneBe

19-48575989-C-T

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_177973.2(SULT2B1):c.120C>T(p.Pro40=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 1,613,536 control chromosomes in the GnomAD database, including 20,560 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 2214 hom., cov: 30)
Exomes 𝑓: 0.15 ( 18346 hom. )

Consequence

SULT2B1
NM_177973.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.55
Variant links:
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 -21 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 19-48575989-C-T is Benign according to our data. Variant chr19-48575989-C-T is described in ClinVar as [Benign]. Clinvar id is 1613054.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-2.55 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SULT2B1NM_177973.2 linkuse as main transcriptc.120C>T p.Pro40= synonymous_variant 2/7 ENST00000201586.7
SULT2B1NM_004605.2 linkuse as main transcriptc.75C>T p.Pro25= synonymous_variant 1/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SULT2B1ENST00000201586.7 linkuse as main transcriptc.120C>T p.Pro40= synonymous_variant 2/71 NM_177973.2 P2O00204-1
SULT2B1ENST00000323090.4 linkuse as main transcriptc.75C>T p.Pro25= synonymous_variant 1/61 A2O00204-2
ENST00000666424.1 linkuse as main transcriptn.493+20757G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.160
AC:
24232
AN:
151884
Hom.:
2214
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.222
Gnomad AMI
AF:
0.0362
Gnomad AMR
AF:
0.106
Gnomad ASJ
AF:
0.171
Gnomad EAS
AF:
0.00212
Gnomad SAS
AF:
0.121
Gnomad FIN
AF:
0.106
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.158
Gnomad OTH
AF:
0.155
GnomAD3 exomes
AF:
0.130
AC:
32296
AN:
248900
Hom.:
2453
AF XY:
0.132
AC XY:
17769
AN XY:
134738
show subpopulations
Gnomad AFR exome
AF:
0.224
Gnomad AMR exome
AF:
0.0720
Gnomad ASJ exome
AF:
0.177
Gnomad EAS exome
AF:
0.00256
Gnomad SAS exome
AF:
0.127
Gnomad FIN exome
AF:
0.112
Gnomad NFE exome
AF:
0.155
Gnomad OTH exome
AF:
0.129
GnomAD4 exome
AF:
0.154
AC:
225448
AN:
1461536
Hom.:
18346
Cov.:
32
AF XY:
0.153
AC XY:
111531
AN XY:
727074
show subpopulations
Gnomad4 AFR exome
AF:
0.223
Gnomad4 AMR exome
AF:
0.0770
Gnomad4 ASJ exome
AF:
0.183
Gnomad4 EAS exome
AF:
0.000907
Gnomad4 SAS exome
AF:
0.129
Gnomad4 FIN exome
AF:
0.115
Gnomad4 NFE exome
AF:
0.164
Gnomad4 OTH exome
AF:
0.155
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.160
AC:
24256
AN:
152000
Hom.:
2214
Cov.:
30
AF XY:
0.156
AC XY:
11608
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.222
Gnomad4 AMR
AF:
0.105
Gnomad4 ASJ
AF:
0.171
Gnomad4 EAS
AF:
0.00213
Gnomad4 SAS
AF:
0.121
Gnomad4 FIN
AF:
0.106
Gnomad4 NFE
AF:
0.158
Gnomad4 OTH
AF:
0.153
Alfa
AF:
0.159
Hom.:
4061
Bravo
AF:
0.161
Asia WGS
AF:
0.0630
AC:
219
AN:
3478
EpiCase
AF:
0.157
EpiControl
AF:
0.159

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

SULT2B1-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesOct 22, 2019This variant is classified as 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 submitterclinical testingInvitaeJan 29, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.61
Cadd
Benign
2.7
Dann
Benign
0.84

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2544794; hg19: chr19-49079246; API