chr3-71046963-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001349338.3(FOXP1):c.643C>G(p.Pro215Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00114 in 1,614,070 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001349338.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXP1 | NM_001349338.3 | c.643C>G | p.Pro215Ala | missense_variant | Exon 10 of 21 | ENST00000649528.3 | NP_001336267.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXP1 | ENST00000649528.3 | c.643C>G | p.Pro215Ala | missense_variant | Exon 10 of 21 | NM_001349338.3 | ENSP00000497369.1 | |||
ENSG00000285708 | ENST00000647725.1 | c.643C>G | p.Pro215Ala | missense_variant | Exon 15 of 26 | ENSP00000497585.1 |
Frequencies
GnomAD3 genomes AF: 0.00114 AC: 173AN: 152174Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000924 AC: 232AN: 251026Hom.: 0 AF XY: 0.000914 AC XY: 124AN XY: 135640
GnomAD4 exome AF: 0.00114 AC: 1672AN: 1461778Hom.: 3 Cov.: 32 AF XY: 0.00114 AC XY: 826AN XY: 727194
GnomAD4 genome AF: 0.00114 AC: 173AN: 152292Hom.: 1 Cov.: 32 AF XY: 0.00122 AC XY: 91AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:3
This variant is associated with the following publications: (PMID: 19352412, 20848658, 20950788, 26647308) -
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FOXP1: BS1 -
not specified Benign:1
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FOXP1-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). -
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at