rs62443106

Positions:

• chr7-37917102-C-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000476620.1(ENSG00000290149):​c.-37-31738C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0281 in 152,262 control chromosomes in the GnomAD database, including 98 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 0.028 (98 hom., cov: 32)
• Consequence: ENSG00000290149 ENST00000476620.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.882

Genes affected

ENSG00000290149 (HGNC:):

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.37917102C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290149	ENST00000476620.1	c.-37-31738C>A		intron_variant		4		ENSP00000425858.1
SFRP4	ENST00000447200.2	c.44-2649G>T		intron_variant		5		ENSP00000402262.2

Frequencies

GnomAD3 genomes AF: 0.0281 AC: 4274 AN: 152144 Hom.: 97 Cov.: 32

Gnomad AFR AF: 0.0281

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0179

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.0873

Gnomad SAS AF: 0.0695

Gnomad FIN AF: 0.0254

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0246

Gnomad OTH AF: 0.0239

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

GnomAD4 genome AF: 0.0281 AC: 4277 AN: 152262 Hom.: 98 Cov.: 32 AF XY: 0.0293 AC XY: 2183 AN XY: 74454

Gnomad4 AFR AF: 0.0281

Gnomad4 AMR AF: 0.0178

Gnomad4 ASJ AF: 0.00980

Gnomad4 EAS AF: 0.0875

Gnomad4 SAS AF: 0.0692

Gnomad4 FIN AF: 0.0254

Gnomad4 NFE AF: 0.0246

Gnomad4 OTH AF: 0.0256

Alfa AF: 0.0236 Hom.: 6

Bravo AF: 0.0273

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	13
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62443106; hg19: chr7-37956704;