chr11-18269809-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_199161.5(SAA1):āc.323A>Gā(p.Lys108Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0125 in 1,608,608 control chromosomes in the GnomAD database, including 150 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_199161.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SAA1 | NM_199161.5 | c.323A>G | p.Lys108Arg | missense_variant | 4/4 | ENST00000356524.9 | NP_954630.2 | |
SAA1 | NM_000331.6 | c.323A>G | p.Lys108Arg | missense_variant | 4/4 | NP_000322.3 | ||
SAA1 | NM_001178006.3 | c.323A>G | p.Lys108Arg | missense_variant | 5/5 | NP_001171477.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SAA1 | ENST00000356524.9 | c.323A>G | p.Lys108Arg | missense_variant | 4/4 | 1 | NM_199161.5 | ENSP00000348918.4 |
Frequencies
GnomAD3 genomes AF: 0.00997 AC: 1490AN: 149496Hom.: 5 Cov.: 33
GnomAD3 exomes AF: 0.0104 AC: 2622AN: 251476Hom.: 18 AF XY: 0.0102 AC XY: 1393AN XY: 135914
GnomAD4 exome AF: 0.0128 AC: 18619AN: 1458990Hom.: 145 Cov.: 35 AF XY: 0.0125 AC XY: 9106AN XY: 726014
GnomAD4 genome AF: 0.00995 AC: 1488AN: 149618Hom.: 5 Cov.: 33 AF XY: 0.00953 AC XY: 698AN XY: 73224
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2024 | SAA1: BP4, BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at