rs10510286

chr3-4103345-A-Cchr3-4103345-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011533624.4(SUMF1):c.1015-34600T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,076 control chromosomes in the GnomAD database, including 3,718 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 0.15 (3718 hom., cov: 32)
• Consequence: SUMF1 XM_011533624.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUMF1	XM_011533624.4	c.1015-34600T>G		intron_variant
SUMF1	XM_017006252.3	c.955-34600T>G		intron_variant
SUMF1	XM_017006253.2	c.940-34600T>G		intron_variant
SUMF1	XM_017006254.3	c.1015-34600T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUMF1	ENST00000448413.5	c.1015-34600T>G		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22823 AN: 151958 Hom.: 3694 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0154

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0301

Gnomad OTH AF: 0.121

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.151 AC: 22895 AN: 152076 Hom.: 3718 Cov.: 32 AF XY: 0.149 AC XY: 11090 AN XY: 74328

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.0141

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0154

Gnomad4 NFE AF: 0.0301

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0988 Hom.: 269

Bravo AF: 0.175

Asia WGS AF: 0.153 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.11
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510286; hg19: chr3-4145029;