2-133287894-G-C

Variant names:

• chr2-133287894-G-C
• rs13002346
• NM_207363.3:c.143+15143C>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+15143C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,112 control chromosomes in the GnomAD database, including 1,076 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 0.10 (1076 hom., cov: 32)
• Consequence: NCKAP5 NM_207363.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428
• Publications: 4 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 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+15143C>G		intron	N/A	NP_997246.2
	NCKAP5	NM_207481.4		c.143+15143C>G		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+15143C>G		intron	N/A	ENSP00000387128.1
	NCKAP5	ENST00000427594.5	TSL:1	c.128+15143C>G		intron	N/A	ENSP00000399070.1
	NCKAP5	ENST00000409213.5	TSL:5	c.143+15143C>G		intron	N/A	ENSP00000386952.1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15624 AN: 151994 Hom.: 1078 Cov.: 32

Gnomad AFR AF: 0.0279

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0684

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.103 AC: 15621 AN: 152112 Hom.: 1076 Cov.: 32 AF XY: 0.101 AC XY: 7512 AN XY: 74364

African (AFR) AF: 0.0278 AC: 1155 AN: 41490

American (AMR) AF: 0.109 AC: 1669 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 407 AN: 3472

East Asian (EAS) AF: 0.121 AC: 628 AN: 5182

South Asian (SAS) AF: 0.0691 AC: 332 AN: 4804

European-Finnish (FIN) AF: 0.124 AC: 1311 AN: 10564

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9708 AN: 67996

Other (OTH) AF: 0.132 AC: 278 AN: 2114

Alfa AF: 0.0525 Hom.: 47

Bravo AF: 0.0984

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.62
PhyloP100		0.43
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: rs13002346; hg19: chr2-134045466;