chr2-189689541-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001378068.1(ANKAR):c.616A>G(p.Thr206Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0011 in 1,577,898 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0062 ( 17 hom., cov: 32)
Exomes 𝑓: 0.00056 ( 11 hom. )
Consequence
ANKAR
NM_001378068.1 missense
NM_001378068.1 missense
Scores
5
12
Clinical Significance
Conservation
PhyloP100: 4.29
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.005278468).
BP6
?
Variant 2-189689541-A-G is Benign according to our data. Variant chr2-189689541-A-G is described in ClinVar as [Benign]. Clinvar id is 716762.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00616 (938/152322) while in subpopulation AFR AF= 0.021 (874/41562). AF 95% confidence interval is 0.0199. There are 17 homozygotes in gnomad4. There are 450 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 17 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKAR | NM_001378068.1 | c.616A>G | p.Thr206Ala | missense_variant | 3/23 | ENST00000684021.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKAR | ENST00000684021.1 | c.616A>G | p.Thr206Ala | missense_variant | 3/23 | NM_001378068.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00616 AC: 938AN: 152204Hom.: 17 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00168 AC: 371AN: 221296Hom.: 4 AF XY: 0.00126 AC XY: 151AN XY: 120164
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GnomAD4 exome AF: 0.000564 AC: 804AN: 1425576Hom.: 11 Cov.: 31 AF XY: 0.000448 AC XY: 317AN XY: 707256
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GnomAD4 genome ? AF: 0.00616 AC: 938AN: 152322Hom.: 17 Cov.: 32 AF XY: 0.00604 AC XY: 450AN XY: 74480
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Asia WGS
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Uncertain
D;D
Polyphen
B;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at