6-4069007-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173563.3(FAM217A):āc.1216T>Cā(p.Ser406Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,458 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_173563.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM217A | NM_173563.3 | c.1216T>C | p.Ser406Pro | missense_variant | 7/7 | ENST00000274673.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM217A | ENST00000274673.8 | c.1216T>C | p.Ser406Pro | missense_variant | 7/7 | 1 | NM_173563.3 | P2 | |
FAM217A | ENST00000639338.1 | c.1618T>C | p.Ser540Pro | missense_variant | 9/9 | 5 | A2 | ||
FAM217A | ENST00000380188.2 | n.1625T>C | non_coding_transcript_exon_variant | 5/5 | 2 | ||||
FAM217A | ENST00000469157.5 | n.391+4268T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250508Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135462
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461458Hom.: 0 Cov.: 39 AF XY: 0.00000275 AC XY: 2AN XY: 726952
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2024 | The c.1216T>C (p.S406P) alteration is located in exon 7 (coding exon 6) of the FAM217A gene. This alteration results from a T to C substitution at nucleotide position 1216, causing the serine (S) at amino acid position 406 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at