1-15296753-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001391957.1(FHAD1):c.638C>T(p.Ala213Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000419 in 1,551,748 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001391957.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FHAD1 | NM_001391957.1 | c.638C>T | p.Ala213Val | missense_variant | Exon 5 of 34 | ENST00000688493.1 | NP_001378886.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FHAD1 | ENST00000688493.1 | c.638C>T | p.Ala213Val | missense_variant | Exon 5 of 34 | NM_001391957.1 | ENSP00000509124.1 |
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 152002Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000636 AC: 10AN: 157318Hom.: 0 AF XY: 0.0000841 AC XY: 7AN XY: 83210
GnomAD4 exome AF: 0.0000414 AC: 58AN: 1399628Hom.: 2 Cov.: 31 AF XY: 0.0000406 AC XY: 28AN XY: 690314
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.638C>T (p.A213V) alteration is located in exon 5 (coding exon 4) of the FHAD1 gene. This alteration results from a C to T substitution at nucleotide position 638, causing the alanine (A) at amino acid position 213 to be replaced by a valine (V). 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