rs11125895
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001201543.2(FAM161A):āc.321A>Gā(p.Ile107Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 1,612,636 control chromosomes in the GnomAD database, including 28,342 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_001201543.2 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 | UniProt |
---|---|---|---|---|---|---|---|
FAM161A | NM_001201543.2 | c.321A>G | p.Ile107Met | missense_variant | 2/7 | ENST00000404929.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM161A | ENST00000404929.6 | c.321A>G | p.Ile107Met | missense_variant | 2/7 | 1 | NM_001201543.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.164 AC: 24937AN: 152084Hom.: 2172 Cov.: 32
GnomAD3 exomes AF: 0.182 AC: 45380AN: 249384Hom.: 4305 AF XY: 0.182 AC XY: 24638AN XY: 135316
GnomAD4 exome AF: 0.188 AC: 274156AN: 1460434Hom.: 26175 Cov.: 32 AF XY: 0.187 AC XY: 136033AN XY: 726616
GnomAD4 genome ? AF: 0.164 AC: 24933AN: 152202Hom.: 2167 Cov.: 32 AF XY: 0.162 AC XY: 12069AN XY: 74398
ClinVar
Submissions by phenotype
Retinitis pigmentosa 28 Benign:2
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 20, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 10, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Retinal dystrophy Benign:1
Benign, criteria provided, single submitter | research | Dept Of Ophthalmology, Nagoya University | Oct 01, 2023 | - - |
Retinitis pigmentosa Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at