chr2-169531430-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024622.6(FASTKD1):c.2249C>T(p.Ala750Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000295 in 1,612,240 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024622.6 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 |
---|---|---|---|---|---|---|---|
FASTKD1 | NM_024622.6 | c.2249C>T | p.Ala750Val | missense_variant | 13/15 | ENST00000453153.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASTKD1 | ENST00000453153.7 | c.2249C>T | p.Ala750Val | missense_variant | 13/15 | 1 | NM_024622.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000224 AC: 34AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000259 AC: 65AN: 250848Hom.: 0 AF XY: 0.000251 AC XY: 34AN XY: 135586
GnomAD4 exome AF: 0.000302 AC: 441AN: 1460006Hom.: 1 Cov.: 30 AF XY: 0.000282 AC XY: 205AN XY: 726334
GnomAD4 genome AF: 0.000223 AC: 34AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74426
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2022 | The c.2249C>T (p.A750V) alteration is located in exon 13 (coding exon 12) of the FASTKD1 gene. This alteration results from a C to T substitution at nucleotide position 2249, causing the alanine (A) at amino acid position 750 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