rs981928115
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001145715.3(KPNA7):āc.15T>Cā(p.Asp5=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,551,232 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00015 ( 0 hom., cov: 31)
Exomes š: 0.000016 ( 0 hom. )
Consequence
KPNA7
NM_001145715.3 synonymous
NM_001145715.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.30
Genes affected
KPNA7 (HGNC:21839): (karyopherin subunit alpha 7) The transport of molecules between the nucleus and the cytoplasm in eukaryotic cells is mediated by the nuclear pore complex (NPC), which consists of 60-100 proteins. Small molecules (up to 70 kD) can pass through the nuclear pore by nonselective diffusion while larger molecules are transported by an active process. The protein encoded by this gene belongs to the importin alpha family, and is involved in nuclear protein import, but exhibits different nuclear localization signal binding specificity compared to other members of the family. A pseudogene of this gene has been defined on chromosome 5. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 7-99207452-A-G is Benign according to our data. Variant chr7-99207452-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 415826.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.3 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KPNA7 | NM_001145715.3 | c.15T>C | p.Asp5= | synonymous_variant | 2/11 | ENST00000327442.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KPNA7 | ENST00000327442.7 | c.15T>C | p.Asp5= | synonymous_variant | 2/11 | 1 | NM_001145715.3 | P1 | |
KPNA7 | ENST00000681060.1 | c.15T>C | p.Asp5= | synonymous_variant | 2/11 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 151924Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000192 AC: 3AN: 156554Hom.: 0 AF XY: 0.0000362 AC XY: 3AN XY: 82974
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GnomAD4 exome AF: 0.0000164 AC: 23AN: 1399308Hom.: 0 Cov.: 31 AF XY: 0.0000188 AC XY: 13AN XY: 690162
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GnomAD4 genome ? AF: 0.000151 AC: 23AN: 151924Hom.: 0 Cov.: 31 AF XY: 0.000135 AC XY: 10AN XY: 74190
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at