NM_207363.3:c.429+9277A>C

Variant names:

• chr2-132984875-T-G
• rs2320399
• NM_207363.3:c.429+9277A>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+9277A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 148,926 control chromosomes in the GnomAD database, including 16,290 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 0.44 (16290 hom., cov: 25)
• Consequence: NCKAP5 NM_207363.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 5 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 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+9277A>C		intron	N/A	NP_997246.2
	NCKAP5	NM_207481.4		c.429+9277A>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+9277A>C		intron	N/A	ENSP00000387128.1
	NCKAP5	ENST00000409213.5	TSL:5	c.429+9277A>C		intron	N/A	ENSP00000386952.1

Frequencies

GnomAD3 genomes AF: 0.443 AC: 65949 AN: 148808 Hom.: 16292 Cov.: 25

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.443 AC: 65946 AN: 148926 Hom.: 16290 Cov.: 25 AF XY: 0.440 AC XY: 31905 AN XY: 72448

African (AFR) AF: 0.254 AC: 10250 AN: 40332

American (AMR) AF: 0.399 AC: 5844 AN: 14650

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1875 AN: 3442

East Asian (EAS) AF: 0.124 AC: 637 AN: 5120

South Asian (SAS) AF: 0.492 AC: 2250 AN: 4570

European-Finnish (FIN) AF: 0.558 AC: 5667 AN: 10150

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 37829 AN: 67440

Other (OTH) AF: 0.444 AC: 901 AN: 2030

Alfa AF: 0.509 Hom.: 62763

Bravo AF: 0.418

Asia WGS AF: 0.318 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.6
DANN	Benign	0.31
PhyloP100		0.038
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: rs2320399; hg19: chr2-133742448;