rs1052981

chr7-37906899-G-A

Variant summary

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

The NM_003014.4(SFRP4):c.*580C>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 0.702 in 152,070 control chromosomes in the GnomAD database, including 37,853 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 0.70 (37853 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: SFRP4 NM_003014.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFRP4	NM_003014.4	c.*580C>T		3_prime_UTR_variant	6/6	ENST00000436072.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFRP4	ENST00000436072.7	c.*580C>T		3_prime_UTR_variant	6/6	1	NM_003014.4	P1

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106750 AN: 151952 Hom.: 37833 Cov.: 31

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.720

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.702 AC: 106807 AN: 152070 Hom.: 37853 Cov.: 31 AF XY: 0.699 AC XY: 52003 AN XY: 74358

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.756

Gnomad4 OTH AF: 0.715

Alfa AF: 0.736 Hom.: 30590

Bravo AF: 0.694

Asia WGS AF: 0.690 AC: 2396 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.44
Dann	Benign	0.48

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: rs1052981; hg19: chr7-37946501;