rs10494174

Positions:

Variant summary

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

The NM_182760.4(SUMF1):​c.954+7113G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0282 in 152,274 control chromosomes in the GnomAD database, including 98 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 0.028 ( 98 hom., cov: 32)

Consequence

SUMF1
NM_182760.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.467
Variant links:
Genes affected
SUMF1 (HGNC:20376): (sulfatase modifying factor 1) This gene encodes an enzyme that catalyzes the hydrolysis of sulfate esters by oxidizing a cysteine residue in the substrate sulfatase to an active site 3-oxoalanine residue, which is also known as C-alpha-formylglycine. Mutations in this gene cause multiple sulfatase deficiency, a lysosomal storage disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]

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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0596 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SUMF1NM_182760.4 linkuse as main transcriptc.954+7113G>A intron_variant ENST00000272902.10 NP_877437.2 Q8NBK3-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SUMF1ENST00000272902.10 linkuse as main transcriptc.954+7113G>A intron_variant 1 NM_182760.4 ENSP00000272902.5 Q8NBK3-1

Frequencies

GnomAD3 genomes
AF:
0.0281
AC:
4273
AN:
152156
Hom.:
96
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0614
Gnomad AMI
AF:
0.0461
Gnomad AMR
AF:
0.0274
Gnomad ASJ
AF:
0.00778
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00786
Gnomad FIN
AF:
0.0204
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0137
Gnomad OTH
AF:
0.0258
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0282
AC:
4287
AN:
152274
Hom.:
98
Cov.:
32
AF XY:
0.0280
AC XY:
2085
AN XY:
74462
show subpopulations
Gnomad4 AFR
AF:
0.0616
Gnomad4 AMR
AF:
0.0274
Gnomad4 ASJ
AF:
0.00778
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00787
Gnomad4 FIN
AF:
0.0204
Gnomad4 NFE
AF:
0.0137
Gnomad4 OTH
AF:
0.0255
Alfa
AF:
0.0158
Hom.:
30
Bravo
AF:
0.0311
Asia WGS
AF:
0.0130
AC:
44
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.62
DANN
Benign
0.22

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: rs10494174; hg19: chr3-4445436; API