chr20-58461548-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153360.3(APCDD1L):c.748G>A(p.Val250Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000133 in 1,418,332 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V250L) has been classified as Uncertain significance.
Frequency
Consequence
NM_153360.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APCDD1L | NM_153360.3 | c.748G>A | p.Val250Met | missense_variant | 4/4 | ENST00000371149.8 | |
APCDD1L | NM_001304787.2 | c.781G>A | p.Val261Met | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APCDD1L | ENST00000371149.8 | c.748G>A | p.Val250Met | missense_variant | 4/4 | 1 | NM_153360.3 | P1 | |
APCDD1L | ENST00000491015.1 | n.159G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000965 AC: 7AN: 72510Hom.: 0 AF XY: 0.0000833 AC XY: 3AN XY: 35994
GnomAD4 exome AF: 0.000138 AC: 175AN: 1266212Hom.: 0 Cov.: 30 AF XY: 0.000143 AC XY: 87AN XY: 610222
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.748G>A (p.V250M) alteration is located in exon 4 (coding exon 4) of the APCDD1L gene. This alteration results from a G to A substitution at nucleotide position 748, causing the valine (V) at amino acid position 250 to be replaced by a methionine (M). 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