chr19-4199764-C-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001393985.1(ANKRD24):​c.118C>G​(p.Arg40Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000722 in 1,384,456 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R40C) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 7.2e-7 ( 0 hom. )

Consequence

ANKRD24
NM_001393985.1 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.267
Variant links:
Genes affected
ANKRD24 (HGNC:29424): (ankyrin repeat domain 24)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.05698195).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ANKRD24NM_001393985.1 linkc.118C>G p.Arg40Gly missense_variant Exon 3 of 22 ENST00000318934.9 NP_001380914.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ANKRD24ENST00000318934.9 linkc.118C>G p.Arg40Gly missense_variant Exon 3 of 22 5 NM_001393985.1 ENSP00000321731.4 Q8TF21-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
7.22e-7
AC:
1
AN:
1384456
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
682596
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.30e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.17
BayesDel_addAF
Benign
-0.24
T
BayesDel_noAF
Benign
-0.59
CADD
Benign
18
DANN
Benign
0.96
DEOGEN2
Benign
0.0032
T;T
Eigen
Benign
-0.68
Eigen_PC
Benign
-0.55
FATHMM_MKL
Benign
0.68
D
LIST_S2
Benign
0.36
.;T
M_CAP
Benign
0.037
D
MetaRNN
Benign
0.057
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.69
N;N
PrimateAI
Benign
0.46
T
PROVEAN
Benign
-1.3
.;N
REVEL
Benign
0.010
Sift
Benign
0.15
.;T
Sift4G
Benign
0.43
T;T
Polyphen
0.0050
B;B
Vest4
0.28
MutPred
0.34
Loss of MoRF binding (P = 0.0152);Loss of MoRF binding (P = 0.0152);
MVP
0.099
MPC
0.33
ClinPred
0.054
T
GERP RS
0.82
Varity_R
0.079
gMVP
0.37

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.20
Details are displayed if max score is > 0.2
DS_DL_spliceai
0.20
Position offset: 5

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs60004310; hg19: chr19-4199761; API