rs17817190

Positions:

• chr2-133594077-T-G

Variant summary

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

The XM_005263660.5(NCKAP5):​c.-62+47280A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0777 in 152,286 control chromosomes in the GnomAD database, including 493 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 0.078 (493 hom., cov: 33)
• Consequence: NCKAP5 XM_005263660.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NCKAP5	XM_005263660.5	c.-62+47280A>C		intron_variant			XP_005263717.1
NCKAP5	XM_011511099.4	c.-129-34960A>C		intron_variant			XP_011509401.1
NCKAP5	XM_011511100.4	c.-129-34960A>C		intron_variant			XP_011509402.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0778 AC: 11837 AN: 152168 Hom.: 492 Cov.: 33

Gnomad AFR AF: 0.0484

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0582

Gnomad EAS AF: 0.0309

Gnomad SAS AF: 0.0497

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0841

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

GnomAD4 genome AF: 0.0777 AC: 11839 AN: 152286 Hom.: 493 Cov.: 33 AF XY: 0.0753 AC XY: 5605 AN XY: 74462

Gnomad4 AFR AF: 0.0484

Gnomad4 AMR AF: 0.0773

Gnomad4 ASJ AF: 0.0582

Gnomad4 EAS AF: 0.0309

Gnomad4 SAS AF: 0.0495

Gnomad4 FIN AF: 0.0733

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0837

Alfa AF: 0.0955 Hom.: 966

Bravo AF: 0.0760

Asia WGS AF: 0.0590 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.5
DANN	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17817190; hg19: chr2-134351648;