rs13399558

Variant names:

• chr2-133285643-T-A
• rs13399558
• NM_207363.3:c.143+17394A>T

Your query was ambiguous. Multiple possible variants found:

• chr2-133285643-T-A
• chr2-133285643-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_207363.3(NCKAP5):​c.143+17394A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,096 control chromosomes in the GnomAD database, including 1,752 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 0.15 (1752 hom., cov: 32)
• Consequence: NCKAP5 NM_207363.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• 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]

NCKAP5-AS2 (HGNC:54065): (NCKAP5 antisense RNA 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 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.143+17394A>T		intron	N/A	NP_997246.2
	NCKAP5	NM_207481.4		c.143+17394A>T		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.143+17394A>T		intron	N/A	ENSP00000387128.1
	NCKAP5	ENST00000427594.5	TSL:1	c.128+17394A>T		intron	N/A	ENSP00000399070.1
	NCKAP5	ENST00000409213.5	TSL:5	c.143+17394A>T		intron	N/A	ENSP00000386952.1

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23046 AN: 151978 Hom.: 1745 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.152 AC: 23087 AN: 152096 Hom.: 1752 Cov.: 32 AF XY: 0.151 AC XY: 11226 AN XY: 74354

African (AFR) AF: 0.171 AC: 7076 AN: 41458

American (AMR) AF: 0.154 AC: 2360 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 417 AN: 3468

East Asian (EAS) AF: 0.156 AC: 802 AN: 5154

South Asian (SAS) AF: 0.159 AC: 767 AN: 4810

European-Finnish (FIN) AF: 0.122 AC: 1289 AN: 10594

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.146 AC: 9938 AN: 68004

Other (OTH) AF: 0.155 AC: 328 AN: 2114

Alfa AF: 0.148 Hom.: 217

Bravo AF: 0.155

Asia WGS AF: 0.179 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	10
DANN	Benign	0.76
PhyloP100		1.5
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: rs13399558; hg19: chr2-134043215;