chr11-27658560-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001709.5(BDNF):c.5C>T(p.Thr2Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00221 in 1,614,178 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T2N) has been classified as Uncertain significance.
Frequency
Consequence
NM_001709.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BDNF | NM_001709.5 | c.5C>T | p.Thr2Ile | missense_variant | 2/2 | ENST00000356660.9 | |
BDNF-AS | NR_033312.1 | n.527+98G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BDNF | ENST00000356660.9 | c.5C>T | p.Thr2Ile | missense_variant | 2/2 | 1 | NM_001709.5 | P4 | |
BDNF-AS | ENST00000651238.1 | n.601+98G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00133 AC: 202AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00129 AC: 323AN: 250832Hom.: 1 AF XY: 0.00134 AC XY: 182AN XY: 135758
GnomAD4 exome AF: 0.00230 AC: 3364AN: 1461856Hom.: 7 Cov.: 33 AF XY: 0.00228 AC XY: 1655AN XY: 727232
GnomAD4 genome AF: 0.00132 AC: 201AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.00103 AC XY: 77AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Apr 27, 2019 | - - |
Obesity Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Congenital central hypoventilation Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | Feb 01, 2002 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
BDNF-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 01, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at