2-132984759-A-G

Variant names:

• chr2-132984759-A-G
• rs6704839
• NM_207363.3:c.429+9393T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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]

ACMG classification

Our verdict: Benign. The variant received -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.

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.429+9393T>C		intron	N/A	NP_997246.2
	NCKAP5	NM_207481.4		c.429+9393T>C		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.429+9393T>C		intron	N/A	ENSP00000387128.1
	NCKAP5	ENST00000409213.5	TSL:5	c.429+9393T>C		intron	N/A	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

African (AFR) AF: 0.308 AC: 12714 AN: 41250

American (AMR) AF: 0.404 AC: 6116 AN: 15132

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1732 AN: 3468

East Asian (EAS) AF: 0.536 AC: 2756 AN: 5140

South Asian (SAS) AF: 0.473 AC: 2255 AN: 4768

European-Finnish (FIN) AF: 0.546 AC: 5699 AN: 10446

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37075 AN: 67904

Other (OTH) AF: 0.438 AC: 920 AN: 2102

Alfa AF: 0.457 Hom.: 5162

Bravo AF: 0.443

Asia WGS AF: 0.487 AC: 1693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		0.34
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: rs6704839; hg19: chr2-133742332;