4-124669583-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020337.3(ANKRD50):āc.3694A>Gā(p.Ile1232Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000211 in 1,613,488 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_020337.3 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 |
---|---|---|---|---|---|---|---|
ANKRD50 | NM_020337.3 | c.3694A>G | p.Ile1232Val | missense_variant | 4/5 | ENST00000504087.6 | |
ANKRD50 | NM_001167882.2 | c.3157A>G | p.Ile1053Val | missense_variant | 3/4 | ||
ANKRD50 | XM_017008471.2 | c.3694A>G | p.Ile1232Val | missense_variant | 3/4 | ||
ANKRD50 | XM_047415992.1 | c.3694A>G | p.Ile1232Val | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKRD50 | ENST00000504087.6 | c.3694A>G | p.Ile1232Val | missense_variant | 4/5 | 2 | NM_020337.3 | P1 | |
ANKRD50 | ENST00000515641.1 | c.3157A>G | p.Ile1053Val | missense_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000204 AC: 51AN: 250520Hom.: 0 AF XY: 0.000258 AC XY: 35AN XY: 135424
GnomAD4 exome AF: 0.000220 AC: 321AN: 1461254Hom.: 1 Cov.: 34 AF XY: 0.000234 AC XY: 170AN XY: 726946
GnomAD4 genome AF: 0.000125 AC: 19AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74432
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2021 | The c.3694A>G (p.I1232V) alteration is located in exon 4 (coding exon 3) of the ANKRD50 gene. This alteration results from a A to G substitution at nucleotide position 3694, causing the isoleucine (I) at amino acid position 1232 to be replaced by a valine (V). 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