rs3242

chr8-41262035-G-Achr8-41262035-G-C

Variant summary

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

The NM_003012.5(SFRP1):c.*3132C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,260 control chromosomes in the GnomAD database, including 6,980 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 0.29 (6970 hom., cov: 33)
  • Exomes 𝑓: 0.32 (10 hom.)
• Consequence: SFRP1 NM_003012.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45

Genes affected

SFRP1 (HGNC:10776): (secreted frizzled related protein 1) 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. Members of this family act as soluble modulators of Wnt signaling; epigenetic silencing of SFRP genes leads to deregulated activation of the Wnt-pathway which is associated with cancer. This gene may also be involved in determining the polarity of photoreceptor cells in the retina. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFRP1	NM_003012.5	c.*3132C>T		3_prime_UTR_variant	3/3	ENST00000220772.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFRP1	ENST00000220772.8	c.*3132C>T		3_prime_UTR_variant	3/3	1	NM_003012.5	P1
SFRP1	ENST00000379845.3	c.*3132C>T		3_prime_UTR_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44000 AN: 151948 Hom.: 6976 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.0732

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.322

GnomAD4 exome AF: 0.325 AC: 63 AN: 194 Hom.: 10 Cov.: 0 AF XY: 0.317 AC XY: 40 AN XY: 126

Gnomad4 FIN exome AF: 0.321

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.289 AC: 44006 AN: 152066 Hom.: 6970 Cov.: 33 AF XY: 0.285 AC XY: 21172 AN XY: 74320

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.0735

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.322

Alfa AF: 0.316 Hom.: 4746

Bravo AF: 0.276

Asia WGS AF: 0.167 AC: 582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	12
Dann	Benign	0.77

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

Other links and lift over

dbSNP: rs3242; hg19: chr8-41119554;