2-105803165-T-G

Variant names:

• chr2-105803165-T-G
• rs10496403
• NM_003581.5:c.-200-13265T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003581.5(NCK2):​c.-200-13265T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,070 control chromosomes in the GnomAD database, including 3,982 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 0.22 (3982 hom., cov: 32)
• Consequence: NCK2 NM_003581.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.785
• Publications: 3 publications found

Genes affected

NCK2 (HGNC:7665): (NCK adaptor protein 2) This gene encodes a member of the NCK family of adaptor proteins. The protein contains three SH3 domains and one SH2 domain. The protein has no known catalytic function but has been shown to bind and recruit various proteins involved in the regulation of receptor protein tyrosine kinases. It is through these regulatory activities that this protein is believed to be involved in cytoskeletal reorganization. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCK2	NM_003581.5	c.-200-13265T>G		intron_variant	Intron 1 of 4	ENST00000233154.9	NP_003572.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCK2	ENST00000233154.9	c.-200-13265T>G		intron_variant	Intron 1 of 4	5	NM_003581.5	ENSP00000233154.4
NCK2	ENST00000393348.6	c.-200-13265T>G		intron_variant	Intron 1 of 3	3		ENSP00000377017.2
NCK2	ENST00000451463.6	c.-200-13265T>G		intron_variant	Intron 1 of 3	2		ENSP00000410428.2

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33370 AN: 151952 Hom.: 3978 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.220 AC: 33394 AN: 152070 Hom.: 3982 Cov.: 32 AF XY: 0.223 AC XY: 16585 AN XY: 74332

African (AFR) AF: 0.134 AC: 5568 AN: 41484

American (AMR) AF: 0.193 AC: 2956 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 826 AN: 3466

East Asian (EAS) AF: 0.280 AC: 1448 AN: 5170

South Asian (SAS) AF: 0.330 AC: 1592 AN: 4826

European-Finnish (FIN) AF: 0.290 AC: 3055 AN: 10552

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17143 AN: 67964

Other (OTH) AF: 0.208 AC: 440 AN: 2112

Alfa AF: 0.244 Hom.: 17973

Bravo AF: 0.210

Asia WGS AF: 0.277 AC: 962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	9.9
DANN	Benign	0.82
PhyloP100		0.79
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: rs10496403; hg19: chr2-106419622;