chrX-8795423-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_174951.3(FAM9A):c.489-3C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00689 in 1,181,120 control chromosomes in the GnomAD database, including 21 homozygotes. There are 2,632 hemizygotes in GnomAD. 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 Benign (★).
Frequency
Consequence
NM_174951.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM9A | NM_174951.3 | c.489-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000381003.7 | |||
FAM9A | NM_001171186.1 | c.489-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM9A | ENST00000381003.7 | c.489-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_174951.3 | P1 | |||
FAM9A | ENST00000543214.1 | c.489-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00519 AC: 580AN: 111669Hom.: 1 Cov.: 22 AF XY: 0.00561 AC XY: 190AN XY: 33841
GnomAD3 exomes AF: 0.00549 AC: 909AN: 165488Hom.: 5 AF XY: 0.00547 AC XY: 296AN XY: 54126
GnomAD4 exome AF: 0.00707 AC: 7564AN: 1069398Hom.: 20 Cov.: 30 AF XY: 0.00715 AC XY: 2442AN XY: 341732
GnomAD4 genome AF: 0.00517 AC: 578AN: 111722Hom.: 1 Cov.: 22 AF XY: 0.00560 AC XY: 190AN XY: 33904
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 14, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at