rs1800497
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_178510.2(ANKK1):c.2137G>A(p.Glu713Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152052 control chromosomes in the gnomAD Genomes database, including 5529 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.26 ( 5529 hom., cov: 34)
Exomes 𝑓: 0.26 ( 9971 hom. )
Consequence
ANKK1
NM_178510.2 missense
NM_178510.2 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: 0.438
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=6.9350004E-4).
BP6
?
Variant 11-113400106-G-A is Benign according to our data. Variant chr11-113400106-G-A is described in ClinVar as [Benign]. Clinvar id is 2105. Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKK1 | NM_178510.2 | c.2137G>A | p.Glu713Lys | missense_variant | 8/8 | ENST00000303941.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKK1 | ENST00000303941.4 | c.2137G>A | p.Glu713Lys | missense_variant | 8/8 | 1 | NM_178510.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.258 AC: 39295AN: 152052Hom.: 5529 Cov.: 34
GnomAD3 genomes
AF:
AC:
39295
AN:
152052
Hom.:
Cov.:
34
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.264 AC: 65225AN: 246888Hom.: 9971 AF XY: 0.254 AC XY: 34091AN XY: 134200
GnomAD3 exomes
AF:
AC:
65225
AN:
246888
Hom.:
AF XY:
AC XY:
34091
AN XY:
134200
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.219 AC: 320284AN: 1460472Hom.: 38093 AF XY: 0.219 AC XY: 159389AN XY: 726500
GnomAD4 exome
AF:
AC:
320284
AN:
1460472
Hom.:
AF XY:
AC XY:
159389
AN XY:
726500
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
723
ALSPAC
AF:
AC:
718
ESP6500AA
AF:
AC:
1351
ESP6500EA
AF:
AC:
1598
ExAC
AF:
AC:
31010
Asia WGS
AF:
AC:
1207
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 16, 2013 | - - |
Taq1A POLYMORPHISM Benign:1
Benign, no assertion criteria provided | literature only | OMIM | Oct 17, 2008 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
P
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
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