X-13040870-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_174901.6(FAM9C):c.217G>A(p.Asp73Asn) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 1,126,163 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_174901.6 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM9C | NM_174901.6 | c.217G>A | p.Asp73Asn | missense_variant, splice_region_variant | 5/8 | ENST00000380625.8 | |
FAM9C | XM_024452348.2 | c.529G>A | p.Asp177Asn | missense_variant, splice_region_variant | 5/7 | ||
FAM9C | XM_005274460.4 | c.217G>A | p.Asp73Asn | missense_variant, splice_region_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM9C | ENST00000380625.8 | c.217G>A | p.Asp73Asn | missense_variant, splice_region_variant | 5/8 | 1 | NM_174901.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000713 AC: 8AN: 112161Hom.: 0 Cov.: 23 AF XY: 0.0000582 AC XY: 2AN XY: 34351
GnomAD3 exomes AF: 0.0000142 AC: 2AN: 140889Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 37909
GnomAD4 exome AF: 0.00000789 AC: 8AN: 1013951Hom.: 0 Cov.: 20 AF XY: 0.00000337 AC XY: 1AN XY: 297151
GnomAD4 genome AF: 0.0000713 AC: 8AN: 112212Hom.: 0 Cov.: 23 AF XY: 0.0000581 AC XY: 2AN XY: 34412
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2023 | The c.217G>A (p.D73N) alteration is located in exon 5 (coding exon 4) of the FAM9C gene. This alteration results from a G to A substitution at nucleotide position 217, causing the aspartic acid (D) at amino acid position 73 to be replaced by an asparagine (N). 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