rs764690820

Variant summary

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

The NM_001282771.3(ANKMY1):​c.3037G>T​(p.Val1013Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,455,320 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. 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. V1013M) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

ANKMY1
NM_001282771.3 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.81
Variant links:
Genes affected
ANKMY1 (HGNC:20987): (ankyrin repeat and MYND domain containing 1) Predicted to enable metal ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

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=0.060822546).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ANKMY1NM_001282771.3 linkc.3037G>T p.Val1013Leu missense_variant Exon 17 of 18 ENST00000401804.6 NP_001269700.1 J3KQ21

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ANKMY1ENST00000401804.6 linkc.3037G>T p.Val1013Leu missense_variant Exon 17 of 18 1 NM_001282771.3 ENSP00000385887.1 J3KQ21

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000399
AC:
1
AN:
250878
Hom.:
0
AF XY:
0.00000738
AC XY:
1
AN XY:
135592
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000881
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1455320
Hom.:
0
Cov.:
31
AF XY:
0.00000138
AC XY:
1
AN XY:
722512
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:
0.00000181
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.28
T
BayesDel_noAF
Benign
-0.64
CADD
Benign
0.0010
DANN
Benign
0.45
DEOGEN2
Benign
0.0099
T;.;T;.;.;.
Eigen
Benign
-1.6
Eigen_PC
Benign
-1.7
FATHMM_MKL
Benign
0.029
N
LIST_S2
Benign
0.61
T;T;T;T;T;T
M_CAP
Benign
0.0085
T
MetaRNN
Benign
0.061
T;T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.20
.;.;N;.;.;.
PrimateAI
Benign
0.23
T
PROVEAN
Benign
-0.010
N;N;N;N;N;N
REVEL
Benign
0.0070
Sift
Benign
0.30
T;T;T;T;T;T
Sift4G
Benign
0.35
T;T;T;T;T;T
Polyphen
0.0
B;B;B;B;.;.
Vest4
0.081
MutPred
0.25
.;.;Loss of loop (P = 0.1242);.;.;.;
MVP
0.25
ClinPred
0.046
T
GERP RS
-5.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.040
gMVP
0.34

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs764690820; hg19: chr2-241420363; API