chr1-63323249-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_012183.3(FOXD3):c.191C>A(p.Ala64Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 1,520,138 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXD3 | NM_012183.3 | c.191C>A | p.Ala64Glu | missense_variant | 1/1 | ENST00000371116.4 | |
FOXD3-AS1 | NR_121637.1 | n.87+1106G>T | intron_variant, non_coding_transcript_variant | ||||
FOXD3-AS1 | NR_121636.1 | n.185+242G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXD3 | ENST00000371116.4 | c.191C>A | p.Ala64Glu | missense_variant | 1/1 | NM_012183.3 | P1 | ||
FOXD3-AS1 | ENST00000427268.1 | n.87+1106G>T | intron_variant, non_coding_transcript_variant | 1 | |||||
FOXD3-AS1 | ENST00000431294.7 | n.286+242G>T | intron_variant, non_coding_transcript_variant | 1 | |||||
FOXD3-AS1 | ENST00000697579.1 | n.203+224G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152100Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000890 AC: 1AN: 112384Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 62026
GnomAD4 exome AF: 0.00000219 AC: 3AN: 1368038Hom.: 0 Cov.: 33 AF XY: 0.00000297 AC XY: 2AN XY: 674408
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152100Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2024 | The c.191C>A (p.A64E) alteration is located in exon 1 (coding exon 1) of the FOXD3 gene. This alteration results from a C to A substitution at nucleotide position 191, causing the alanine (A) at amino acid position 64 to be replaced by a glutamic acid (E). 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