rs62443106

Variant names:

• chr7-37917102-C-A
• rs62443106
• ENST00000476620.1:c.-37-31738C>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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290149	ENST00000476620.1	c.-37-31738C>A		intron_variant	Intron 2 of 3	4		ENSP00000425858.1
SFRP4	ENST00000447200.2	c.44-2649G>T		intron_variant	Intron 2 of 5	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;