chr2-132942736-G-T

Position:

• chr2-132942736-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_207363.3(NCKAP5):​c.579+20984C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 151,922 control chromosomes in the GnomAD database, including 28,517 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.57 (28517 hom., cov: 32)
• Consequence: NCKAP5 NM_207363.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

Genes affected

NCKAP5 (HGNC:29847): (NCK associated protein 5) Predicted to be involved in microtubule bundle formation and microtubule depolymerization. Predicted to be active in microtubule plus-end. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NCKAP5	NM_207363.3	c.579+20984C>A		intron_variant		ENST00000409261.6	NP_997246.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NCKAP5	ENST00000409261.6	c.579+20984C>A		intron_variant		5	NM_207363.3	ENSP00000387128.1
NCKAP5	ENST00000409213.5	c.579+20984C>A		intron_variant		5		ENSP00000386952.1

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86838 AN: 151806 Hom.: 28509 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.553

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.572 AC: 86865 AN: 151922 Hom.: 28517 Cov.: 32 AF XY: 0.576 AC XY: 42738 AN XY: 74258

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.558

Alfa AF: 0.663 Hom.: 33811

Bravo AF: 0.526

Asia WGS AF: 0.618 AC: 2147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	9.3
DANN	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs281575; hg19: chr2-133700309;