chr6-46753832-A-G
Position:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001162435.3(ANKRD66):āc.274A>Gā(p.Ile92Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000599 in 1,551,704 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00034 ( 0 hom., cov: 32)
Exomes š: 0.000029 ( 0 hom. )
Consequence
ANKRD66
NM_001162435.3 missense
NM_001162435.3 missense
Scores
1
14
Clinical Significance
Conservation
PhyloP100: 6.07
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.025936306).
BP6
Variant 6-46753832-A-G is Benign according to our data. Variant chr6-46753832-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2466097.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKRD66 | NM_001162435.3 | c.274A>G | p.Ile92Val | missense_variant | 4/5 | ENST00000565422.3 | |
ANKRD66 | XM_017010148.2 | c.421A>G | p.Ile141Val | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKRD66 | ENST00000565422.3 | c.274A>G | p.Ile92Val | missense_variant | 4/5 | 2 | NM_001162435.3 | P1 | |
ANKRD66 | ENST00000445060.1 | c.88A>G | p.Ile30Val | missense_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 152182Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
52
AN:
152182
Hom.:
Cov.:
32
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: 0.0000714 AC: 11AN: 154022Hom.: 0 AF XY: 0.0000612 AC XY: 5AN XY: 81726
GnomAD3 exomes
AF:
AC:
11
AN:
154022
Hom.:
AF XY:
AC XY:
5
AN XY:
81726
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: 0.0000293 AC: 41AN: 1399404Hom.: 0 Cov.: 31 AF XY: 0.0000203 AC XY: 14AN XY: 690212
GnomAD4 exome
AF:
AC:
41
AN:
1399404
Hom.:
Cov.:
31
AF XY:
AC XY:
14
AN XY:
690212
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:
GnomAD4 genome AF: 0.000341 AC: 52AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74486
GnomAD4 genome
AF:
AC:
52
AN:
152300
Hom.:
Cov.:
32
AF XY:
AC XY:
23
AN XY:
74486
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ESP6500AA
AF:
AC:
2
ESP6500EA
AF:
AC:
0
ExAC
AF:
AC:
3
Asia WGS
AF:
AC:
1
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N
Sift
Benign
T
Sift4G
Benign
T
Vest4
MVP
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