1-6614100-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153812.3(PHF13):c.34C>G(p.Pro12Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000227 in 1,599,940 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153812.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHF13 | NM_153812.3 | c.34C>G | p.Pro12Ala | missense_variant | Exon 1 of 4 | ENST00000377648.5 | NP_722519.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PHF13 | ENST00000377648.5 | c.34C>G | p.Pro12Ala | missense_variant | Exon 1 of 4 | 1 | NM_153812.3 | ENSP00000366876.4 | ||
KLHL21 | ENST00000467612.5 | c.-81+350G>C | intron_variant | Intron 1 of 3 | 3 | ENSP00000466089.1 | ||||
KLHL21 | ENST00000463043.1 | c.-81+350G>C | intron_variant | Intron 1 of 3 | 5 | ENSP00000466479.1 | ||||
PHF13 | ENST00000495385.1 | n.339C>G | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 151862Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000487 AC: 11AN: 225706Hom.: 0 AF XY: 0.0000561 AC XY: 7AN XY: 124698
GnomAD4 exome AF: 0.000236 AC: 342AN: 1448078Hom.: 1 Cov.: 33 AF XY: 0.000246 AC XY: 177AN XY: 720514
GnomAD4 genome AF: 0.000138 AC: 21AN: 151862Hom.: 0 Cov.: 30 AF XY: 0.000108 AC XY: 8AN XY: 74162
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.34C>G (p.P12A) alteration is located in exon 1 (coding exon 1) of the PHF13 gene. This alteration results from a C to G substitution at nucleotide position 34, causing the proline (P) at amino acid position 12 to be replaced by an alanine (A). 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