4-123256160-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_145207.3(AFG2A):c.2485G>T(p.Asp829Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00769 in 1,614,010 control chromosomes in the GnomAD database, including 100 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_145207.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AFG2A | NM_145207.3 | c.2485G>T | p.Asp829Tyr | missense_variant | 15/16 | ENST00000274008.5 | NP_660208.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPATA5 | ENST00000274008.5 | c.2485G>T | p.Asp829Tyr | missense_variant | 15/16 | 1 | NM_145207.3 | ENSP00000274008.3 | ||
SPATA5 | ENST00000675612.1 | c.2554G>T | p.Asp852Tyr | missense_variant | 16/17 | ENSP00000502453.1 |
Frequencies
GnomAD3 genomes AF: 0.00632 AC: 962AN: 152114Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.0118 AC: 2952AN: 251172Hom.: 46 AF XY: 0.0108 AC XY: 1461AN XY: 135732
GnomAD4 exome AF: 0.00783 AC: 11445AN: 1461778Hom.: 96 Cov.: 30 AF XY: 0.00767 AC XY: 5576AN XY: 727180
GnomAD4 genome AF: 0.00633 AC: 964AN: 152232Hom.: 4 Cov.: 32 AF XY: 0.00611 AC XY: 455AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 19, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 29, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jan 26, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 03, 2019 | - - |
Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 03, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at