chr15-49328675-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152647.3(FAM227B):c.1420C>T(p.Arg474Cys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000315 in 1,554,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict 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 Uncertain significance (★).
Frequency
Consequence
NM_152647.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM227B | NM_152647.3 | c.1420C>T | p.Arg474Cys | missense_variant, splice_region_variant | 16/16 | ENST00000299338.11 | |
GALK2 | NM_002044.4 | c.*516G>A | 3_prime_UTR_variant | 10/10 | ENST00000560031.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM227B | ENST00000299338.11 | c.1420C>T | p.Arg474Cys | missense_variant, splice_region_variant | 16/16 | 2 | NM_152647.3 | P1 | |
GALK2 | ENST00000560031.6 | c.*516G>A | 3_prime_UTR_variant | 10/10 | 1 | NM_002044.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152056Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000782 AC: 13AN: 166170Hom.: 0 AF XY: 0.0000574 AC XY: 5AN XY: 87088
GnomAD4 exome AF: 0.0000335 AC: 47AN: 1402692Hom.: 0 Cov.: 32 AF XY: 0.0000361 AC XY: 25AN XY: 692392
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152056Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74258
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 10, 2022 | The c.1420C>T (p.R474C) alteration is located in exon 16 (coding exon 15) of the FAM227B gene. This alteration results from a C to T substitution at nucleotide position 1420, causing the arginine (R) at amino acid position 474 to be replaced by a cysteine (C). 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