chr2-182935332-A-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_013436.5(NCKAP1):c.2739T>C(p.Ile913=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00494 in 1,590,640 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0032 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0051 ( 30 hom. )
Consequence
NCKAP1
NM_013436.5 synonymous
NM_013436.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.07
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 -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
?
Variant 2-182935332-A-G is Benign according to our data. Variant chr2-182935332-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2651738.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.07 with no splicing effect.
BS2
?
High AC in GnomAd at 490 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCKAP1 | NM_013436.5 | c.2739T>C | p.Ile913= | synonymous_variant | 25/31 | ENST00000361354.9 | |
NCKAP1 | NM_205842.3 | c.2757T>C | p.Ile919= | synonymous_variant | 26/32 | ||
NCKAP1 | XM_006712200.4 | c.2751T>C | p.Ile917= | synonymous_variant | 26/32 | ||
NCKAP1 | XM_006712201.4 | c.2733T>C | p.Ile911= | synonymous_variant | 25/31 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCKAP1 | ENST00000361354.9 | c.2739T>C | p.Ile913= | synonymous_variant | 25/31 | 1 | NM_013436.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00322 AC: 490AN: 152190Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00336 AC: 772AN: 229850Hom.: 3 AF XY: 0.00358 AC XY: 447AN XY: 124994
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GnomAD4 exome AF: 0.00512 AC: 7367AN: 1438332Hom.: 30 Cov.: 28 AF XY: 0.00516 AC XY: 3692AN XY: 715208
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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 | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | NCKAP1: BP4, BP7, BS2 - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at