chr17-49502059-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002507.4(NGFR):c.67-4C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000425 in 1,340,598 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_002507.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NGFR | NM_002507.4 | c.67-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000172229.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NGFR | ENST00000172229.8 | c.67-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002507.4 | P1 | |||
NGFR | ENST00000504201.1 | c.-216-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
NGFR | ENST00000509200.5 | c.-216-4C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00191 AC: 272AN: 142638Hom.: 1 Cov.: 30
GnomAD3 exomes AF: 0.000492 AC: 120AN: 244004Hom.: 2 AF XY: 0.000455 AC XY: 60AN XY: 131932
GnomAD4 exome AF: 0.000246 AC: 295AN: 1197842Hom.: 2 Cov.: 35 AF XY: 0.000233 AC XY: 137AN XY: 587242
GnomAD4 genome ? AF: 0.00193 AC: 275AN: 142756Hom.: 2 Cov.: 30 AF XY: 0.00188 AC XY: 130AN XY: 69102
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at