rs71546610

chr7-37916793-G-Achr7-37916793-G-C

Variant summary

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

The NM_003014.4(SFRP4):c.-256C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 574,606 control chromosomes in the GnomAD database, including 18,657 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 0.27 (5570 hom., cov: 33)
  • Exomes 𝑓: 0.25 (13087 hom.)
• Consequence: SFRP4 NM_003014.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477

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=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFRP4	NM_003014.4	c.-256C>T		5_prime_UTR_variant	1/6	ENST00000436072.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFRP4	ENST00000436072.7	c.-256C>T		5_prime_UTR_variant	1/6	1	NM_003014.4	P1
SFRP4	ENST00000447200.2	c.44-2340C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40780 AN: 152072 Hom.: 5558 Cov.: 33

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.256

GnomAD4 exome AF: 0.245 AC: 103580 AN: 422416 Hom.: 13087 Cov.: 4 AF XY: 0.245 AC XY: 54151 AN XY: 221362

Gnomad4 AFR exome AF: 0.347

Gnomad4 AMR exome AF: 0.277

Gnomad4 ASJ exome AF: 0.272

Gnomad4 EAS exome AF: 0.218

Gnomad4 SAS exome AF: 0.236

Gnomad4 FIN exome AF: 0.216

Gnomad4 NFE exome AF: 0.244

Gnomad4 OTH exome AF: 0.249

GnomAD4 genome AF: 0.268 AC: 40833 AN: 152190 Hom.: 5570 Cov.: 33 AF XY: 0.266 AC XY: 19769 AN XY: 74412

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.255

Alfa AF: 0.260 Hom.: 688

Bravo AF: 0.279

Asia WGS AF: 0.238 AC: 826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
Cadd	Benign	8.1
Dann	Benign	0.92

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: rs71546610; hg19: chr7-37956395; COSMIC: COSV52260123; COSMIC: COSV52260123;