rs2072445
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000172229.8(NGFR):c.569-62G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.092 in 1,593,668 control chromosomes in the GnomAD database, including 7,234 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.076 ( 558 hom., cov: 32)
Exomes 𝑓: 0.094 ( 6676 hom. )
Consequence
NGFR
ENST00000172229.8 intron
ENST00000172229.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.117
Genes affected
NGFR (HGNC:7809): (nerve growth factor receptor) Nerve growth factor receptor contains an extracellular domain containing four 40-amino acid repeats with 6 cysteine residues at conserved positions followed by a serine/threonine-rich region, a single transmembrane domain, and a 155-amino acid cytoplasmic domain. The cysteine-rich region contains the nerve growth factor binding domain. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NGFR | NM_002507.4 | c.569-62G>T | intron_variant | ENST00000172229.8 | NP_002498.1 | |||
NGFR-AS1 | NR_103773.1 | n.377+633C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NGFR | ENST00000172229.8 | c.569-62G>T | intron_variant | 1 | NM_002507.4 | ENSP00000172229 | P1 | |||
NGFR-AS1 | ENST00000514506.1 | n.377+633C>A | intron_variant, non_coding_transcript_variant | 2 | ||||||
NGFR | ENST00000504201.1 | c.287-62G>T | intron_variant | 2 | ENSP00000421731 |
Frequencies
GnomAD3 genomes AF: 0.0765 AC: 11633AN: 152044Hom.: 557 Cov.: 32
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GnomAD4 exome AF: 0.0936 AC: 134914AN: 1441506Hom.: 6676 AF XY: 0.0951 AC XY: 67883AN XY: 714170
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GnomAD4 genome AF: 0.0765 AC: 11636AN: 152162Hom.: 558 Cov.: 32 AF XY: 0.0767 AC XY: 5708AN XY: 74398
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at