2-132774526-G-T

Variant names:

• chr2-132774526-G-T
• rs7603615
• NM_207363.3:c.5050-632C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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]

ENSG00000286068 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207363.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCKAP5	NM_207363.3	MANE Select	c.5050-632C>A		intron	N/A	NP_997246.2
	NCKAP5	NM_207481.4		c.1093-632C>A		intron	N/A	NP_997364.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCKAP5	ENST00000409261.6	TSL:5 MANE Select	c.5050-632C>A		intron	N/A	ENSP00000387128.1
	NCKAP5	ENST00000409213.5	TSL:5	c.1093-632C>A		intron	N/A	ENSP00000386952.1
	NCKAP5	ENST00000473859.1	TSL:3	n.262+6526C>A		intron	N/A

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

African (AFR) AF: 0.248 AC: 10257 AN: 41344

American (AMR) AF: 0.130 AC: 1988 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.00922 AC: 32 AN: 3470

East Asian (EAS) AF: 0.126 AC: 650 AN: 5152

South Asian (SAS) AF: 0.0897 AC: 430 AN: 4794

European-Finnish (FIN) AF: 0.0466 AC: 492 AN: 10552

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00610 AC: 415 AN: 67978

Other (OTH) AF: 0.0762 AC: 161 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.46
PhyloP100		0.73
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7603615; hg19: chr2-133532099;