chr5-77035562-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_018046.5(AGGF1):c.335A>G(p.Tyr112Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000392 in 1,612,806 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_018046.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGGF1 | NM_018046.5 | c.335A>G | p.Tyr112Cys | missense_variant | 3/14 | ENST00000312916.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGGF1 | ENST00000312916.12 | c.335A>G | p.Tyr112Cys | missense_variant | 3/14 | 1 | NM_018046.5 | P1 | |
AGGF1 | ENST00000506806.1 | c.335A>G | p.Tyr112Cys | missense_variant | 3/3 | 1 | |||
AGGF1 | ENST00000502408.1 | c.*61A>G | 3_prime_UTR_variant, NMD_transcript_variant | 3/5 | 1 | ||||
AGGF1 | ENST00000503538.5 | n.352A>G | non_coding_transcript_exon_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00145 AC: 221AN: 152200Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000522 AC: 131AN: 250744Hom.: 0 AF XY: 0.000354 AC XY: 48AN XY: 135594
GnomAD4 exome AF: 0.000281 AC: 411AN: 1460488Hom.: 0 Cov.: 30 AF XY: 0.000233 AC XY: 169AN XY: 726636
GnomAD4 genome ? AF: 0.00146 AC: 222AN: 152318Hom.: 2 Cov.: 33 AF XY: 0.00141 AC XY: 105AN XY: 74486
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 26, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at