chr5-7865993-A-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024091.4(FASTKD3):c.1439-10T>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 1,607,630 control chromosomes in the GnomAD database, including 29,745 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_024091.4 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FASTKD3 | NM_024091.4 | c.1439-10T>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000264669.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASTKD3 | ENST00000264669.10 | c.1439-10T>A | splice_polypyrimidine_tract_variant, intron_variant | 2 | NM_024091.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.143 AC: 21599AN: 150722Hom.: 1926 Cov.: 32
GnomAD3 exomes AF: 0.143 AC: 36031AN: 251214Hom.: 3288 AF XY: 0.146 AC XY: 19821AN XY: 135782
GnomAD4 exome AF: 0.186 AC: 271119AN: 1456790Hom.: 27816 Cov.: 29 AF XY: 0.184 AC XY: 133542AN XY: 725054
GnomAD4 genome AF: 0.143 AC: 21618AN: 150840Hom.: 1929 Cov.: 32 AF XY: 0.141 AC XY: 10356AN XY: 73570
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at