chr4-124670317-C-G
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020337.3(ANKRD50):āc.2960G>Cā(p.Cys987Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,672 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 32)
Exomes š: 6.8e-7 ( 0 hom. )
Consequence
ANKRD50
NM_020337.3 missense
NM_020337.3 missense
Scores
1
4
14
Clinical Significance
Conservation
PhyloP100: 5.70
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKRD50 | NM_020337.3 | c.2960G>C | p.Cys987Ser | missense_variant | 4/5 | ENST00000504087.6 | |
ANKRD50 | NM_001167882.2 | c.2423G>C | p.Cys808Ser | missense_variant | 3/4 | ||
ANKRD50 | XM_017008471.2 | c.2960G>C | p.Cys987Ser | missense_variant | 3/4 | ||
ANKRD50 | XM_047415992.1 | c.2960G>C | p.Cys987Ser | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKRD50 | ENST00000504087.6 | c.2960G>C | p.Cys987Ser | missense_variant | 4/5 | 2 | NM_020337.3 | P1 | |
ANKRD50 | ENST00000515641.1 | c.2423G>C | p.Cys808Ser | missense_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461672Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 727140
GnomAD4 exome
AF:
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1
AN:
1461672
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Cov.:
34
AF XY:
AC XY:
1
AN XY:
727140
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.2960G>C (p.C987S) alteration is located in exon 4 (coding exon 3) of the ANKRD50 gene. This alteration results from a G to C substitution at nucleotide position 2960, causing the cysteine (C) at amino acid position 987 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationAssessor
Benign
N;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MutPred
Gain of disorder (P = 0.0126);.;
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.