15-43793946-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The ENST00000409960.6(SERF2):c.487C>A(p.Leu163Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,552,512 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000409960.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERF2 | NM_001018108.4 | c.*173C>A | 3_prime_UTR_variant | 3/3 | ENST00000249786.9 | ||
SERF2-C15ORF63 | NR_037673.1 | n.517+863C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERF2 | ENST00000249786.9 | c.*173C>A | 3_prime_UTR_variant | 3/3 | 1 | NM_001018108.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000126 AC: 2AN: 158242Hom.: 0 AF XY: 0.0000119 AC XY: 1AN XY: 84116
GnomAD4 exome AF: 0.00000500 AC: 7AN: 1400304Hom.: 0 Cov.: 31 AF XY: 0.00000579 AC XY: 4AN XY: 691308
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2022 | The c.487C>A (p.L163I) alteration is located in exon 3 (coding exon 3) of the SERF2 gene. This alteration results from a C to A substitution at nucleotide position 487, causing the leucine (L) at amino acid position 163 to be replaced by an isoleucine (I). 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