7-37907562-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003014.4(SFRP4):c.958C>A(p.Pro320Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 1,612,272 control chromosomes in the GnomAD database, including 135,524 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003014.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SFRP4 | NM_003014.4 | c.958C>A | p.Pro320Thr | missense_variant | 6/6 | ENST00000436072.7 | NP_003005.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SFRP4 | ENST00000436072.7 | c.958C>A | p.Pro320Thr | missense_variant | 6/6 | 1 | NM_003014.4 | ENSP00000410715.2 | ||
ENSG00000290149 | ENST00000476620.1 | c.-37-41278G>T | intron_variant | 4 | ENSP00000425858.1 | |||||
SFRP4 | ENST00000478975.1 | n.326C>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.456 AC: 69168AN: 151686Hom.: 16558 Cov.: 32
GnomAD3 exomes AF: 0.437 AC: 109702AN: 251174Hom.: 24781 AF XY: 0.435 AC XY: 59036AN XY: 135740
GnomAD4 exome AF: 0.400 AC: 583939AN: 1460468Hom.: 118942 Cov.: 35 AF XY: 0.403 AC XY: 292492AN XY: 726542
GnomAD4 genome AF: 0.456 AC: 69240AN: 151804Hom.: 16582 Cov.: 32 AF XY: 0.460 AC XY: 34099AN XY: 74178
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 25, 2021 | This variant is associated with the following publications: (PMID: 26715268) - |
Pyle metaphyseal dysplasia Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
SFRP4-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at