chr2-132774526-G-T

Position:

• chr2-132774526-G-T

Variant summary

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

The NM_207363.3(NCKAP5):​c.5050-632C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.095 in 151,872 control chromosomes in the GnomAD database, including 1,549 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 0.095 (1549 hom., cov: 32)
• Consequence: NCKAP5 NM_207363.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.731

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]

NCKAP5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NCKAP5	NM_207363.3	c.5050-632C>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.5050-632C>A		intron_variant		5	NM_207363.3	ENSP00000387128.1
NCKAP5	ENST00000409213.5	c.1093-632C>A		intron_variant		5		ENSP00000386952.1
NCKAP5	ENST00000473859.1	n.262+6526C>A		intron_variant		3
ENSG00000286068	ENST00000651100.1	n.458-40075G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0948 AC: 14393 AN: 151754 Hom.: 1541 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.00922

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0898

Gnomad FIN AF: 0.0466

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00609

Gnomad OTH AF: 0.0750

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

GnomAD4 genome AF: 0.0950 AC: 14432 AN: 151872 Hom.: 1549 Cov.: 32 AF XY: 0.0978 AC XY: 7257 AN XY: 74214

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.00922

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.0897

Gnomad4 FIN AF: 0.0466

Gnomad4 NFE AF: 0.00610

Gnomad4 OTH AF: 0.0762

Alfa AF: 0.00790 Hom.: 8

Bravo AF: 0.109

Asia WGS AF: 0.155 AC: 539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.46

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: rs7603615; hg19: chr2-133532099;