1-63323938-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_012183.3(FOXD3):c.880G>T(p.Ala294Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000571 in 1,243,186 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012183.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXD3 | NM_012183.3 | c.880G>T | p.Ala294Ser | missense_variant | 1/1 | ENST00000371116.4 | |
FOXD3-AS1 | NR_121637.1 | n.87+417C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXD3 | ENST00000371116.4 | c.880G>T | p.Ala294Ser | missense_variant | 1/1 | NM_012183.3 | P1 | ||
FOXD3-AS1 | ENST00000427268.1 | n.87+417C>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000266 AC: 4AN: 150252Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000613 AC: 67AN: 1092934Hom.: 0 Cov.: 33 AF XY: 0.0000650 AC XY: 34AN XY: 523414
GnomAD4 genome ? AF: 0.0000266 AC: 4AN: 150252Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.880G>T (p.A294S) alteration is located in exon 1 (coding exon 1) of the FOXD3 gene. This alteration results from a G to T substitution at nucleotide position 880, causing the alanine (A) at amino acid position 294 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at