7-37964804-G-T

Variant names:

• chr7-37964804-G-T
• rs1668357
• ENST00000447200.2:c.-52-38030C>A

Variant summary

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

The ENST00000447200.2(SFRP4):​c.-52-38030C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 152,210 control chromosomes in the GnomAD database, including 50,014 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 0.81 (50014 hom., cov: 31)
• Consequence: SFRP4 ENST00000447200.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 13 publications found

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]

SFRP4 Gene-Disease associations (from GenCC):

• Pyle disease

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, PanelApp Australia, Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447200.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFRP4	ENST00000447200.2	TSL:5	c.-52-38030C>A		intron	N/A	ENSP00000402262.2	C9JMJ2

Frequencies

GnomAD3 genomes AF: 0.809 AC: 123065 AN: 152092 Hom.: 49982 Cov.: 31

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.809 AC: 123151 AN: 152210 Hom.: 50014 Cov.: 31 AF XY: 0.807 AC XY: 60038 AN XY: 74394

African (AFR) AF: 0.825 AC: 34268 AN: 41522

American (AMR) AF: 0.789 AC: 12055 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2807 AN: 3472

East Asian (EAS) AF: 0.561 AC: 2896 AN: 5160

South Asian (SAS) AF: 0.812 AC: 3915 AN: 4824

European-Finnish (FIN) AF: 0.837 AC: 8879 AN: 10614

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55628 AN: 68012

Other (OTH) AF: 0.792 AC: 1675 AN: 2114

Alfa AF: 0.820 Hom.: 81679

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.77
DANN	Benign	0.56
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs1668357; hg19: chr7-38004406;