chr7-37964804-G-T

Position:

• chr7-37964804-G-T

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.37964804G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SFRP4	ENST00000447200.2	c.-52-38030C>A		intron_variant		5		ENSP00000402262.2

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

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.812

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.792

Alfa AF: 0.820 Hom.: 63665

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1668357; hg19: chr7-38004406;