rs1802074
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003014.4(SFRP4):c.1019G>A(p.Arg340Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 1,611,698 control chromosomes in the GnomAD database, including 36,456 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 | UniProt |
---|---|---|---|---|---|---|---|
SFRP4 | NM_003014.4 | c.1019G>A | p.Arg340Lys | missense_variant | 6/6 | ENST00000436072.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFRP4 | ENST00000436072.7 | c.1019G>A | p.Arg340Lys | missense_variant | 6/6 | 1 | NM_003014.4 | P1 | |
SFRP4 | ENST00000478975.1 | n.387G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.242 AC: 36804AN: 151968Hom.: 4866 Cov.: 32
GnomAD3 exomes AF: 0.198 AC: 49610AN: 250532Hom.: 5515 AF XY: 0.196 AC XY: 26499AN XY: 135420
GnomAD4 exome AF: 0.204 AC: 298058AN: 1459612Hom.: 31584 Cov.: 32 AF XY: 0.203 AC XY: 147216AN XY: 726192
GnomAD4 genome ? AF: 0.242 AC: 36839AN: 152086Hom.: 4872 Cov.: 32 AF XY: 0.241 AC XY: 17894AN XY: 74324
ClinVar
Submissions by phenotype
Pyle metaphyseal dysplasia Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
SFRP4-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 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