6-112100741-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001033564.3(FAM229B):c.197C>T(p.Thr66Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000669 in 1,613,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001033564.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAM229B | NM_001033564.3 | c.197C>T | p.Thr66Met | missense_variant | 4/4 | ENST00000368656.7 | NP_001028736.1 | |
FAM229B | XM_017011174.3 | c.197C>T | p.Thr66Met | missense_variant | 4/4 | XP_016866663.1 | ||
FAM229B | XM_017011175.3 | c.197C>T | p.Thr66Met | missense_variant | 3/3 | XP_016866664.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAM229B | ENST00000368656.7 | c.197C>T | p.Thr66Met | missense_variant | 4/4 | 1 | NM_001033564.3 | ENSP00000357645.2 | ||
FAM229B | ENST00000604268.1 | c.197C>T | p.Thr66Met | missense_variant | 4/4 | 5 | ENSP00000474987.1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152136Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251372Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135842
GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461716Hom.: 0 Cov.: 30 AF XY: 0.0000688 AC XY: 50AN XY: 727142
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152136Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74314
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at