chr2-133131062-T-C

Position:

• chr2-133131062-T-C

Variant summary

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

The NM_207363.3(NCKAP5):​c.208-951A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,164 control chromosomes in the GnomAD database, including 3,371 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 0.20 (3371 hom., cov: 32)
• Consequence: NCKAP5 NM_207363.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NCKAP5	NM_207363.3	c.208-951A>G		intron_variant		ENST00000409261.6	NP_997246.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NCKAP5	ENST00000409261.6	c.208-951A>G		intron_variant		5	NM_207363.3	ENSP00000387128	P1
NCKAP5	ENST00000427594.5	c.195-951A>G		intron_variant		1		ENSP00000399070
NCKAP5	ENST00000409213.5	c.208-951A>G		intron_variant		5		ENSP00000386952

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30742 AN: 152046 Hom.: 3369 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.202 AC: 30750 AN: 152164 Hom.: 3371 Cov.: 32 AF XY: 0.200 AC XY: 14862 AN XY: 74396

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.197

Alfa AF: 0.226 Hom.: 519

Bravo AF: 0.196

Asia WGS AF: 0.0770 AC: 266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.9
DANN	Benign	0.74

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: rs7598823; hg19: chr2-133888634;