rs10496702

chr2-133247997-G-Achr2-133247997-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_207363.3(NCKAP5):c.144-34218C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,198 control chromosomes in the GnomAD database, including 3,000 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 0.18 (3000 hom., cov: 32)
• Consequence: NCKAP5 NM_207363.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.593

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NCKAP5	NM_207363.3	c.144-34218C>T		intron_variant		ENST00000409261.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NCKAP5	ENST00000409261.6	c.144-34218C>T		intron_variant		5	NM_207363.3	P1
NCKAP5	ENST00000427594.5	c.131-34218C>T		intron_variant		1
NCKAP5	ENST00000358991.4	c.144-34218C>T		intron_variant		5
NCKAP5	ENST00000409213.5	c.144-34218C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27352 AN: 152078 Hom.: 2989 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.0870

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.180 AC: 27412 AN: 152198 Hom.: 3000 Cov.: 32 AF XY: 0.179 AC XY: 13309 AN XY: 74424

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0851

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.181

Alfa AF: 0.131 Hom.: 2505

Bravo AF: 0.194

Asia WGS AF: 0.161 AC: 561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
Cadd	Benign	5.0
Dann	Benign	0.47

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496702; hg19: chr2-134005569;