7-99178073-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001145715.3(KPNA7):c.1318-7G>A 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 0.000932 in 1,551,104 control chromosomes in the GnomAD database, including 18 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_001145715.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KPNA7 | NM_001145715.3 | c.1318-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000327442.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KPNA7 | ENST00000327442.7 | c.1318-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001145715.3 | P1 | |||
KPNA7 | ENST00000681060.1 | c.1318-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | P1 |
Frequencies
GnomAD3 genomes AF: 0.00509 AC: 775AN: 152124Hom.: 10 Cov.: 30
GnomAD3 exomes AF: 0.00120 AC: 187AN: 155562Hom.: 3 AF XY: 0.000994 AC XY: 82AN XY: 82462
GnomAD4 exome AF: 0.000479 AC: 670AN: 1398862Hom.: 8 Cov.: 32 AF XY: 0.000422 AC XY: 291AN XY: 689934
GnomAD4 genome AF: 0.00509 AC: 775AN: 152242Hom.: 10 Cov.: 30 AF XY: 0.00501 AC XY: 373AN XY: 74422
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at