7-37907605-G-A
Variant summary
Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS1
The NM_003014.4(SFRP4):c.915C>T(p.Ala305Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000694 in 1,613,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_003014.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Our verdict: Benign. The variant received -11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SFRP4 | ENST00000436072.7 | c.915C>T | p.Ala305Ala | synonymous_variant | Exon 6 of 6 | 1 | NM_003014.4 | ENSP00000410715.2 | ||
ENSG00000290149 | ENST00000476620.1 | c.-37-41235G>A | intron_variant | Intron 2 of 3 | 4 | ENSP00000425858.1 | ||||
SFRP4 | ENST00000478975.1 | n.283C>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152124Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000323 AC: 81AN: 251156 AF XY: 0.000287 show subpopulations
GnomAD4 exome AF: 0.0000691 AC: 101AN: 1461500Hom.: 0 Cov.: 32 AF XY: 0.0000633 AC XY: 46AN XY: 727052 show subpopulations
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74426 show subpopulations
ClinVar
Submissions by phenotype
not provided Benign:1
- -
SFRP4-related disorder Benign:1
This variant is classified as likely 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