chr17-47545902-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_006310.4(NPEPPS):c.256-7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000188 in 1,539,030 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (★).
Frequency
Consequence
NM_006310.4 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NPEPPS | NM_006310.4 | c.256-7C>T | splice_region_variant, intron_variant | Intron 1 of 22 | ENST00000322157.9 | NP_006301.3 | ||
NPEPPS | NM_001411130.1 | c.256-7C>T | splice_region_variant, intron_variant | Intron 1 of 23 | NP_001398059.1 | |||
NPEPPS | NM_001330257.2 | c.244-7C>T | splice_region_variant, intron_variant | Intron 2 of 23 | NP_001317186.1 | |||
NPEPPS | XM_017025373.1 | c.244-7C>T | splice_region_variant, intron_variant | Intron 2 of 24 | XP_016880862.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPEPPS | ENST00000322157.9 | c.256-7C>T | splice_region_variant, intron_variant | Intron 1 of 22 | 1 | NM_006310.4 | ENSP00000320324.4 | |||
NPEPPS | ENST00000526247.6 | n.244-7C>T | splice_region_variant, intron_variant | Intron 2 of 7 | 3 | ENSP00000433735.1 |
Frequencies
GnomAD3 genomes AF: 0.0000264 AC: 4AN: 151680Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000234 AC: 4AN: 170826Hom.: 0 AF XY: 0.0000331 AC XY: 3AN XY: 90750
GnomAD4 exome AF: 0.0000180 AC: 25AN: 1387232Hom.: 0 Cov.: 30 AF XY: 0.0000205 AC XY: 14AN XY: 683150
GnomAD4 genome AF: 0.0000264 AC: 4AN: 151798Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 74184
ClinVar
Submissions by phenotype
not provided Benign:1
NPEPPS: BP4, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at