rs1437898

Variant names:

• chr2-132989057-A-C
• rs1437898
• NM_207363.3:c.429+5095T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-132989057-A-C
• chr2-132989057-A-G
• chr2-132989057-A-T

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+5095T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,026 control chromosomes in the GnomAD database, including 24,543 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 0.56 (24543 hom., cov: 33)
• Consequence: NCKAP5 NM_207363.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122
• Publications: 11 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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCKAP5	NM_207363.3	c.429+5095T>G		intron_variant	Intron 7 of 19	ENST00000409261.6	NP_997246.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCKAP5	ENST00000409261.6	c.429+5095T>G		intron_variant	Intron 7 of 19	5	NM_207363.3	ENSP00000387128.1
NCKAP5	ENST00000409213.5	c.429+5095T>G		intron_variant	Intron 7 of 17	5		ENSP00000386952.1

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85402 AN: 151908 Hom.: 24550 Cov.: 33

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.562 AC: 85414 AN: 152026 Hom.: 24543 Cov.: 33 AF XY: 0.563 AC XY: 41865 AN XY: 74312

African (AFR) AF: 0.439 AC: 18206 AN: 41468

American (AMR) AF: 0.533 AC: 8143 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2226 AN: 3472

East Asian (EAS) AF: 0.592 AC: 3047 AN: 5146

South Asian (SAS) AF: 0.633 AC: 3048 AN: 4814

European-Finnish (FIN) AF: 0.616 AC: 6518 AN: 10576

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42289 AN: 67966

Other (OTH) AF: 0.555 AC: 1173 AN: 2112

Alfa AF: 0.597 Hom.: 66433

Bravo AF: 0.547

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.8
DANN	Benign	0.72
PhyloP100		0.12
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: rs1437898; hg19: chr2-133746630;