rs2271671
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_013436.5(NCKAP1):c.1762-12C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 1,566,778 control chromosomes in the GnomAD database, including 402,442 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.61 ( 31965 hom., cov: 31)
Exomes 𝑓: 0.72 ( 370477 hom. )
Consequence
NCKAP1
NM_013436.5 intron
NM_013436.5 intron
Scores
2
Splicing: ADA: 0.00008718
2
Clinical Significance
Conservation
PhyloP100: 1.48
Genes affected
NCKAP1 (HGNC:7666): (NCK associated protein 1) Contributes to small GTPase binding activity. Involved in Rac protein signal transduction; positive regulation of Arp2/3 complex-mediated actin nucleation; and positive regulation of lamellipodium assembly. Located in extracellular exosome and focal adhesion. Part of SCAR complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant 2-182962290-G-A is Benign according to our data. Variant chr2-182962290-G-A is described in ClinVar as [Benign]. Clinvar id is 1229018.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NCKAP1 | NM_013436.5 | c.1762-12C>T | intron_variant | ENST00000361354.9 | NP_038464.1 | |||
NCKAP1 | NM_205842.3 | c.1780-12C>T | intron_variant | NP_995314.1 | ||||
NCKAP1 | XM_006712200.4 | c.1774-12C>T | intron_variant | XP_006712263.1 | ||||
NCKAP1 | XM_006712201.4 | c.1756-12C>T | intron_variant | XP_006712264.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NCKAP1 | ENST00000361354.9 | c.1762-12C>T | intron_variant | 1 | NM_013436.5 | ENSP00000355348.3 |
Frequencies
GnomAD3 genomes AF: 0.615 AC: 93292AN: 151770Hom.: 31960 Cov.: 31
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GnomAD3 exomes AF: 0.721 AC: 168599AN: 233730Hom.: 62443 AF XY: 0.726 AC XY: 91922AN XY: 126564
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GnomAD4 exome AF: 0.721 AC: 1020640AN: 1414892Hom.: 370477 Cov.: 28 AF XY: 0.721 AC XY: 508348AN XY: 704616
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GnomAD4 genome AF: 0.614 AC: 93317AN: 151886Hom.: 31965 Cov.: 31 AF XY: 0.621 AC XY: 46111AN XY: 74218
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 17, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at