rs4987024

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_001054.4(SULT1A2):​c.185A>T​(p.Tyr62Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0106 in 1,614,102 control chromosomes in the GnomAD database, including 65 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0077 ( 6 hom., cov: 31)
Exomes 𝑓: 0.011 ( 59 hom. )

Consequence

SULT1A2
NM_001054.4 missense

Scores

2
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.79
Variant links:
Genes affected
SULT1A2 (HGNC:11454): (sulfotransferase family 1A member 2) 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. Two alternatively spliced variants that encode the same protein have been described. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.005838901).
BS2
High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SULT1A2NM_001054.4 linkuse as main transcriptc.185A>T p.Tyr62Phe missense_variant 3/8 ENST00000335715.9 NP_001045.2 P50226

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SULT1A2ENST00000335715.9 linkuse as main transcriptc.185A>T p.Tyr62Phe missense_variant 3/81 NM_001054.4 ENSP00000338742.4 P50226

Frequencies

GnomAD3 genomes
AF:
0.00772
AC:
1174
AN:
152110
Hom.:
6
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00174
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00314
Gnomad ASJ
AF:
0.00173
Gnomad EAS
AF:
0.00771
Gnomad SAS
AF:
0.00830
Gnomad FIN
AF:
0.0160
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.0115
Gnomad OTH
AF:
0.00669
GnomAD3 exomes
AF:
0.00961
AC:
2416
AN:
251448
Hom.:
16
AF XY:
0.00971
AC XY:
1319
AN XY:
135908
show subpopulations
Gnomad AFR exome
AF:
0.00185
Gnomad AMR exome
AF:
0.00226
Gnomad ASJ exome
AF:
0.00208
Gnomad EAS exome
AF:
0.00614
Gnomad SAS exome
AF:
0.00983
Gnomad FIN exome
AF:
0.0164
Gnomad NFE exome
AF:
0.0128
Gnomad OTH exome
AF:
0.00946
GnomAD4 exome
AF:
0.0109
AC:
15996
AN:
1461874
Hom.:
59
Cov.:
32
AF XY:
0.0110
AC XY:
7983
AN XY:
727236
show subpopulations
Gnomad4 AFR exome
AF:
0.00188
Gnomad4 AMR exome
AF:
0.00228
Gnomad4 ASJ exome
AF:
0.00207
Gnomad4 EAS exome
AF:
0.00363
Gnomad4 SAS exome
AF:
0.00852
Gnomad4 FIN exome
AF:
0.0170
Gnomad4 NFE exome
AF:
0.0120
Gnomad4 OTH exome
AF:
0.00982
GnomAD4 genome
AF:
0.00774
AC:
1178
AN:
152228
Hom.:
6
Cov.:
31
AF XY:
0.00750
AC XY:
558
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.00173
Gnomad4 AMR
AF:
0.00314
Gnomad4 ASJ
AF:
0.00173
Gnomad4 EAS
AF:
0.00772
Gnomad4 SAS
AF:
0.00830
Gnomad4 FIN
AF:
0.0160
Gnomad4 NFE
AF:
0.0115
Gnomad4 OTH
AF:
0.00899
Alfa
AF:
0.00802
Hom.:
4
Bravo
AF:
0.00647
TwinsUK
AF:
0.00971
AC:
36
ALSPAC
AF:
0.0127
AC:
49
ESP6500AA
AF:
0.00250
AC:
11
ESP6500EA
AF:
0.00802
AC:
69
ExAC
AF:
0.0104
AC:
1268
Asia WGS
AF:
0.0180
AC:
62
AN:
3478
EpiCase
AF:
0.0101
EpiControl
AF:
0.0108

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.48
T
BayesDel_noAF
Benign
-0.45
CADD
Uncertain
24
DANN
Benign
0.97
DEOGEN2
Benign
0.28
T;T;T;T
Eigen
Benign
0.18
Eigen_PC
Benign
0.087
FATHMM_MKL
Benign
0.062
N
LIST_S2
Benign
0.39
T;.;T;T
MetaRNN
Benign
0.0058
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.6
.;L;L;.
PrimateAI
Uncertain
0.50
T
PROVEAN
Benign
-1.9
N;N;N;N
REVEL
Benign
0.071
Sift
Uncertain
0.017
D;T;T;T
Sift4G
Benign
0.18
T;T;T;T
Polyphen
1.0
.;D;D;.
Vest4
0.23
MPC
0.40
ClinPred
0.024
T
GERP RS
3.5
Varity_R
0.39
gMVP
0.48

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs4987024; hg19: chr16-28606960; COSMIC: COSV57683351; COSMIC: COSV57683351; API