rs1376264

Positions:

• chr7-37918687-G-A

Variant summary

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

The ENST00000447200.2(SFRP4):​c.44-4234C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 151,972 control chromosomes in the GnomAD database, including 5,043 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 0.25 (5043 hom., cov: 32)
• Consequence: SFRP4 ENST00000447200.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

Genes affected

SFRP4 (HGNC:10778): (secreted frizzled related protein 4) Secreted frizzled-related protein 4 (SFRP4) is 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. The expression of SFRP4 in ventricular myocardium correlates with apoptosis related gene expression. [provided by RefSeq, Jul 2008]

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 = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFRP4	ENST00000447200.2	c.44-4234C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37368 AN: 151854 Hom.: 5037 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.246 AC: 37384 AN: 151972 Hom.: 5043 Cov.: 32 AF XY: 0.244 AC XY: 18128 AN XY: 74274

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.244

Alfa AF: 0.298 Hom.: 14167

Bravo AF: 0.233

Asia WGS AF: 0.185 AC: 644 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	0.88
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1376264; hg19: chr7-37958289;