3-3731447-A-G

Position:

• chr3-3731447-A-G

Variant summary

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

The NR_149025.1(LOC100130207):​n.697-28986T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 101,806 control chromosomes in the GnomAD database, including 13,370 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 0.61 (13370 hom., cov: 31)
• Consequence: LOC100130207 NR_149025.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261

Genes affected

LOC100130207 (HGNC:):

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100130207	NR_149025.1	n.697-28986T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUMF1	ENST00000470751.5	n.697-28986T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.608 AC: 61799 AN: 101662 Hom.: 13329 Cov.: 31

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.608 AC: 61914 AN: 101806 Hom.: 13370 Cov.: 31 AF XY: 0.608 AC XY: 30266 AN XY: 49772

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.663

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.591

Alfa AF: 0.331 Hom.: 4483

Bravo AF: 0.408

Asia WGS AF: 0.475 AC: 1637 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7628234; hg19: chr3-3773131;