2-132984759-A-G

Position:

• chr2-132984759-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_207363.3(NCKAP5):​c.429+9393T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 151,416 control chromosomes in the GnomAD database, including 17,007 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 0.46 (17007 hom., cov: 29)
• Consequence: NCKAP5 NM_207363.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NCKAP5	NM_207363.3	c.429+9393T>C		intron_variant		ENST00000409261.6	NP_997246.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NCKAP5	ENST00000409261.6	c.429+9393T>C		intron_variant		5	NM_207363.3	ENSP00000387128.1
NCKAP5	ENST00000409213.5	c.429+9393T>C		intron_variant		5		ENSP00000386952.1

Frequencies

GnomAD3 genomes AF: 0.462 AC: 69891 AN: 151298 Hom.: 17008 Cov.: 29

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.462 AC: 69909 AN: 151416 Hom.: 17007 Cov.: 29 AF XY: 0.463 AC XY: 34210 AN XY: 73920

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.438

Alfa AF: 0.410 Hom.: 2028

Bravo AF: 0.443

Asia WGS AF: 0.487 AC: 1693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.81

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: rs6704839; hg19: chr2-133742332;