rs6265
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001709(BDNF):c.196G>A(p.Val66Met) variant causes a missense change. The variant allele was found at a frequency of 0.153 in 152064 control chromosomes in the gnomAD Genomes database, including 2519 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (โ โ ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: ๐ 0.15 ( 2519 hom., cov: 32)
Exomes ๐: 0.19 ( 6030 hom. )
Consequence
BDNF
NM_001709 missense
NM_001709 missense
Scores
1
7
9
Clinical Significance
Conservation
PhyloP100: 4.94
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0017960966).
BP6
?
Variant 11:27658369-C>T is Benign according to our data. Variant chr11-27658369-C-T is described in ClinVar as [Benign]. Clinvar id is 17697. Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BDNF | NM_001709.5 | c.196G>A | p.Val66Met | missense_variant | 2/2 | ENST00000356660.9 | |
BDNF-AS | NR_033312.1 | n.434C>T | non_coding_transcript_exon_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BDNF | ENST00000356660.9 | c.196G>A | p.Val66Met | missense_variant | 2/2 | 1 | NM_001709.5 | P4 | |
BDNF-AS | ENST00000651238.1 | n.508C>T | non_coding_transcript_exon_variant | 5/8 |
Frequencies
GnomAD3 genomes AF: 0.153 AC: 23190AN: 152064Hom.: 2519 Cov.: 32
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23190
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32
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GnomAD3 exomes AF: 0.195 AC: 48968AN: 251276Hom.: 6030 AF XY: 0.199 AC XY: 26958AN XY: 135806
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GnomAD4 exome AF: 0.190 AC: 277361AN: 1461886Hom.: 28821 AF XY: 0.191 AC XY: 138787AN XY: 727244
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TwinsUK
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715
ALSPAC
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693
ESP6500AA
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184
ESP6500EA
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1640
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23513
Asia WGS
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967
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ClinVar
Significance: Benign
Submissions summary: Benign:3Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 18, 2013 | Benign with respect to pulmonary disease based on high population frequency, Th is variant has been proposed to be associated with a rnage of psychiatric manife stations though the data is not solid and more recent meta-analyses argue agains t a risk effect. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, PreventionGenetics | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 30, 2022 | - - |
Memory impairment, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Dec 13, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Uncertain
D;D;.;D;D;D;D;D;D;.;D;D;D;D;D;D;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.;M;M;M;M;M;M;.;M;M;M;M;M;M;.
MutationTaster
Benign
P;P;P;P;P;P;P;P;P;P;P;P;P;P;P;P;P;P
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N
REVEL
Benign
Sift
Pathogenic
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
Sift4G
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Polyphen
D;D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D
Vest4
MPC
1.6
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at