4-153782444-T-C

Variant names:

• chr4-153782444-T-C
• rs17030434
• NM_003013.3:c.584-689A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003013.3(SFRP2):​c.584-689A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,196 control chromosomes in the GnomAD database, including 2,616 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 0.17 (2616 hom., cov: 32)
• Consequence: SFRP2 NM_003013.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377
• Publications: 14 publications found

Genes affected

SFRP2 (HGNC:10777): (secreted frizzled related protein 2) This gene encodes a member of the SFRP family that contains a cysteine-rich domain homologous to the putative Wnt-binding site of Frizzled proteins. SFRPs act as soluble modulators of Wnt signaling. Methylation of this gene is a potential marker for the presence of colorectal cancer. [provided by RefSeq, Jul 2008]

ENSG00000280241 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFRP2	NM_003013.3	c.584-689A>G		intron_variant	Intron 2 of 2	ENST00000274063.5	NP_003004.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFRP2	ENST00000274063.5	c.584-689A>G		intron_variant	Intron 2 of 2	1	NM_003013.3	ENSP00000274063.4

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26215 AN: 152078 Hom.: 2613 Cov.: 32

Gnomad AFR AF: 0.0982

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.172 AC: 26222 AN: 152196 Hom.: 2616 Cov.: 32 AF XY: 0.173 AC XY: 12878 AN XY: 74396

African (AFR) AF: 0.0982 AC: 4080 AN: 41542

American (AMR) AF: 0.148 AC: 2259 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 480 AN: 3472

East Asian (EAS) AF: 0.385 AC: 1989 AN: 5172

South Asian (SAS) AF: 0.158 AC: 760 AN: 4824

European-Finnish (FIN) AF: 0.256 AC: 2705 AN: 10582

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13464 AN: 67996

Other (OTH) AF: 0.168 AC: 355 AN: 2110

Alfa AF: 0.190 Hom.: 5306

Bravo AF: 0.165

Asia WGS AF: 0.241 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.54
DANN	Benign	0.36
PhyloP100		-0.38
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17030434; hg19: chr4-154703596;