chr2-227531186-T-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_004504.5(AGFG1):c.790T>A(p.Ser264Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000701 in 1,613,710 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004504.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGFG1 | NM_004504.5 | c.790T>A | p.Ser264Thr | missense_variant | 6/13 | ENST00000310078.13 | |
AGFG1 | NM_001135187.2 | c.790T>A | p.Ser264Thr | missense_variant | 6/14 | ||
AGFG1 | NM_001135188.2 | c.790T>A | p.Ser264Thr | missense_variant | 6/13 | ||
AGFG1 | NM_001135189.2 | c.695-2363T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGFG1 | ENST00000310078.13 | c.790T>A | p.Ser264Thr | missense_variant | 6/13 | 1 | NM_004504.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000526 AC: 80AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000394 AC: 99AN: 250962Hom.: 0 AF XY: 0.000428 AC XY: 58AN XY: 135646
GnomAD4 exome AF: 0.000719 AC: 1051AN: 1461404Hom.: 2 Cov.: 30 AF XY: 0.000715 AC XY: 520AN XY: 727008
GnomAD4 genome ? AF: 0.000525 AC: 80AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000457 AC XY: 34AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2022 | The c.790T>A (p.S264T) alteration is located in exon 6 (coding exon 6) of the AGFG1 gene. This alteration results from a T to A substitution at nucleotide position 790, causing the serine (S) at amino acid position 264 to be replaced by a threonine (T). 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