12-54499483-C-G
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_005337.5(NCKAP1L):c.213+18C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000135 in 1,329,590 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 (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
NCKAP1L
NM_005337.5 intron
NM_005337.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.256
Genes affected
NCKAP1L (HGNC:4862): (NCK associated protein 1 like) This gene encodes a member of the HEM family of tissue-specific transmembrane proteins which are highly conserved from invertebrates through mammals. This gene is only expressed in hematopoietic cells. The encoded protein is a part of the Scar/WAVE complex which plays an important role in regulating cell shape in both metazoans and plants. Alternatively spliced transcript variants encoding different isoforms have been found.[provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant 12-54499483-C-G is Benign according to our data. Variant chr12-54499483-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2984615.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NCKAP1L | NM_005337.5 | c.213+18C>G | intron_variant | ENST00000293373.11 | NP_005328.2 | |||
NCKAP1L | NM_001184976.2 | c.63+18C>G | intron_variant | NP_001171905.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NCKAP1L | ENST00000293373.11 | c.213+18C>G | intron_variant | 1 | NM_005337.5 | ENSP00000293373 | P1 | |||
NCKAP1L | ENST00000545638.2 | c.63+18C>G | intron_variant | 2 | ENSP00000445596 | |||||
NCKAP1L | ENST00000548221.5 | c.213+18C>G | intron_variant, NMD_transcript_variant | 2 | ENSP00000447246 | |||||
NCKAP1L | ENST00000547500.1 | n.237+18C>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249854Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135144
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GnomAD4 exome AF: 0.0000144 AC: 17AN: 1177408Hom.: 0 Cov.: 16 AF XY: 0.0000167 AC XY: 10AN XY: 599310
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74346
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Dec 01, 2022 | - - |
Computational scores
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Benign
CADD
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DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at