rs1220702

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005420.3(SULT1E1):​c.497-10C>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 1,583,348 control chromosomes in the GnomAD database, including 11,928 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.12 ( 1151 hom., cov: 32)
Exomes 𝑓: 0.12 ( 10777 hom. )

Consequence

SULT1E1
NM_005420.3 splice_polypyrimidine_tract, intron

Scores

2
Splicing: ADA: 0.006855
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.100
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SULT1E1NM_005420.3 linkuse as main transcriptc.497-10C>G splice_polypyrimidine_tract_variant, intron_variant ENST00000226444.4 NP_005411.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SULT1E1ENST00000226444.4 linkuse as main transcriptc.497-10C>G splice_polypyrimidine_tract_variant, intron_variant 1 NM_005420.3 ENSP00000226444 P1

Frequencies

GnomAD3 genomes
AF:
0.116
AC:
17518
AN:
151238
Hom.:
1149
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0954
Gnomad AMI
AF:
0.0945
Gnomad AMR
AF:
0.0891
Gnomad ASJ
AF:
0.161
Gnomad EAS
AF:
0.000773
Gnomad SAS
AF:
0.0467
Gnomad FIN
AF:
0.240
Gnomad MID
AF:
0.178
Gnomad NFE
AF:
0.126
Gnomad OTH
AF:
0.125
GnomAD3 exomes
AF:
0.108
AC:
26451
AN:
245216
Hom.:
1878
AF XY:
0.108
AC XY:
14400
AN XY:
132770
show subpopulations
Gnomad AFR exome
AF:
0.0923
Gnomad AMR exome
AF:
0.0591
Gnomad ASJ exome
AF:
0.161
Gnomad EAS exome
AF:
0.000111
Gnomad SAS exome
AF:
0.0452
Gnomad FIN exome
AF:
0.227
Gnomad NFE exome
AF:
0.131
Gnomad OTH exome
AF:
0.121
GnomAD4 exome
AF:
0.116
AC:
166284
AN:
1431992
Hom.:
10777
Cov.:
24
AF XY:
0.115
AC XY:
82013
AN XY:
713576
show subpopulations
Gnomad4 AFR exome
AF:
0.0959
Gnomad4 AMR exome
AF:
0.0645
Gnomad4 ASJ exome
AF:
0.163
Gnomad4 EAS exome
AF:
0.000307
Gnomad4 SAS exome
AF:
0.0469
Gnomad4 FIN exome
AF:
0.224
Gnomad4 NFE exome
AF:
0.122
Gnomad4 OTH exome
AF:
0.117
GnomAD4 genome
AF:
0.116
AC:
17531
AN:
151356
Hom.:
1151
Cov.:
32
AF XY:
0.118
AC XY:
8752
AN XY:
73958
show subpopulations
Gnomad4 AFR
AF:
0.0955
Gnomad4 AMR
AF:
0.0891
Gnomad4 ASJ
AF:
0.161
Gnomad4 EAS
AF:
0.000775
Gnomad4 SAS
AF:
0.0463
Gnomad4 FIN
AF:
0.240
Gnomad4 NFE
AF:
0.126
Gnomad4 OTH
AF:
0.124
Alfa
AF:
0.126
Hom.:
234
Bravo
AF:
0.106
Asia WGS
AF:
0.0310
AC:
107
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.65
CADD
Benign
9.3
DANN
Benign
0.70

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.0069
dbscSNV1_RF
Benign
0.14
SpliceAI score (max)
0.19
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: rs1220702; hg19: chr4-70713520; API