chr16-263262-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_032039.4(FAM234A):c.972C>T(p.Ser324=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000881 in 1,612,458 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_032039.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM234A | NM_032039.4 | c.972C>T | p.Ser324= | splice_region_variant, synonymous_variant | 9/13 | ENST00000399932.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM234A | ENST00000399932.8 | c.972C>T | p.Ser324= | splice_region_variant, synonymous_variant | 9/13 | 1 | NM_032039.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 152256Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000125 AC: 31AN: 248032Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 134750
GnomAD4 exome AF: 0.0000794 AC: 116AN: 1460084Hom.: 0 Cov.: 32 AF XY: 0.0000771 AC XY: 56AN XY: 726400
GnomAD4 genome ? AF: 0.000171 AC: 26AN: 152374Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74516
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 22, 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