chr11-47784915-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_015231.3(NUP160):c.3888+7G>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000572 in 1,572,590 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_015231.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP160 | NM_015231.3 | c.3888+7G>C | splice_region_variant, intron_variant | ENST00000378460.7 | |||
NUP160 | NR_134636.3 | n.3935+7G>C | splice_region_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP160 | ENST00000378460.7 | c.3888+7G>C | splice_region_variant, intron_variant | 1 | NM_015231.3 | P1 | |||
NUP160 | ENST00000530326.5 | c.3883+7G>C | splice_region_variant, intron_variant | 5 | |||||
NUP160 | ENST00000694866.1 | c.3990+7G>C | splice_region_variant, intron_variant | ||||||
NUP160 | ENST00000532773.1 | n.342G>C | non_coding_transcript_exon_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000659 AC: 1AN: 151650Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000219 AC: 5AN: 228694Hom.: 0 AF XY: 0.0000242 AC XY: 3AN XY: 123928
GnomAD4 exome AF: 0.00000563 AC: 8AN: 1420940Hom.: 0 Cov.: 28 AF XY: 0.00000566 AC XY: 4AN XY: 706762
GnomAD4 genome ? AF: 0.00000659 AC: 1AN: 151650Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74010
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 25, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at