rs3242

Variant names:

• chr8-41262035-G-A
• rs3242
• NM_003012.5:c.*3132C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-41262035-G-A
• chr8-41262035-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 30 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SFRP1	NM_003012.5	c.*3132C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000220772.8	NP_003003.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFRP1	ENST00000220772.8	c.*3132C>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_003012.5	ENSP00000220772.3
SFRP1	ENST00000379845.3	c.*3132C>T		3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000369174.3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.321 AC: 61 AN: 190

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.198 AC: 8221 AN: 41486

American (AMR) AF: 0.248 AC: 3796 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1522 AN: 3470

East Asian (EAS) AF: 0.0735 AC: 381 AN: 5182

South Asian (SAS) AF: 0.207 AC: 996 AN: 4810

European-Finnish (FIN) AF: 0.368 AC: 3877 AN: 10536

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24169 AN: 67982

Other (OTH) AF: 0.322 AC: 680 AN: 2112

Alfa AF: 0.323 Hom.: 6548

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
PhyloP100		1.5
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: rs3242; hg19: chr8-41119554;