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GeneBe

8-41309004-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_003012.5(SFRP1):c.156C>T(p.Tyr52=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00136 in 1,612,448 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0020 ( 3 hom., cov: 33)
Exomes 𝑓: 0.0013 ( 27 hom. )

Consequence

SFRP1
NM_003012.5 synonymous

Scores

1
1

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.39
Variant links:
Genes affected
SFRP1 (HGNC:10776): (secreted frizzled related protein 1) This gene encodes a member of the SFRP family that contains a cysteine-rich domain homologous to the putative Wnt-binding site of Frizzled proteins. Members of this family act as soluble modulators of Wnt signaling; epigenetic silencing of SFRP genes leads to deregulated activation of the Wnt-pathway which is associated with cancer. This gene may also be involved in determining the polarity of photoreceptor cells in the retina. [provided by RefSeq, Sep 2009]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
Variant 8-41309004-G-A is Benign according to our data. Variant chr8-41309004-G-A is described in ClinVar as [Benign]. Clinvar id is 771425.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.39 with no splicing effect.
BS1
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.00129 (1883/1460130) while in subpopulation AMR AF= 0.0289 (1293/44714). AF 95% confidence interval is 0.0276. There are 27 homozygotes in gnomad4_exome. There are 833 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 309 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SFRP1NM_003012.5 linkuse as main transcriptc.156C>T p.Tyr52= synonymous_variant 1/3 ENST00000220772.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SFRP1ENST00000220772.8 linkuse as main transcriptc.156C>T p.Tyr52= synonymous_variant 1/31 NM_003012.5 P1

Frequencies

GnomAD3 genomes
AF:
0.00200
AC:
304
AN:
152200
Hom.:
3
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000338
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0152
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00775
Gnomad SAS
AF:
0.00103
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000103
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.00490
AC:
1217
AN:
248148
Hom.:
19
AF XY:
0.00373
AC XY:
502
AN XY:
134742
show subpopulations
Gnomad AFR exome
AF:
0.000186
Gnomad AMR exome
AF:
0.0296
Gnomad ASJ exome
AF:
0.000199
Gnomad EAS exome
AF:
0.00803
Gnomad SAS exome
AF:
0.000621
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000888
Gnomad OTH exome
AF:
0.00247
GnomAD4 exome
AF:
0.00129
AC:
1883
AN:
1460130
Hom.:
27
Cov.:
31
AF XY:
0.00115
AC XY:
833
AN XY:
726524
show subpopulations
Gnomad4 AFR exome
AF:
0.000239
Gnomad4 AMR exome
AF:
0.0289
Gnomad4 ASJ exome
AF:
0.000153
Gnomad4 EAS exome
AF:
0.0106
Gnomad4 SAS exome
AF:
0.000719
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000306
Gnomad4 OTH exome
AF:
0.00103
GnomAD4 genome
AF:
0.00203
AC:
309
AN:
152318
Hom.:
3
Cov.:
33
AF XY:
0.00216
AC XY:
161
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.000337
Gnomad4 AMR
AF:
0.0155
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00777
Gnomad4 SAS
AF:
0.00104
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000103
Gnomad4 OTH
AF:
0.00236
Alfa
AF:
0.000690
Hom.:
1
Bravo
AF:
0.00354
Asia WGS
AF:
0.00577
AC:
20
AN:
3478
EpiCase
AF:
0.000273
EpiControl
AF:
0.00

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 06, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.58
CADD
Benign
13
DANN
Uncertain
0.97

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs184528079; hg19: chr8-41166523; API