17-4897868-C-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_153827.5(MINK1):c.*581C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 149,182 control chromosomes in the GnomAD database, including 10,488 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.37 (10451 hom., cov: 25)
  • Exomes 𝑓: 0.32 (37 hom.)
• Consequence: MINK1 NM_153827.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.73

Genes affected

CHRNE (HGNC:1966): (cholinergic receptor nicotinic epsilon subunit) Acetylcholine receptors at mature mammalian neuromuscular junctions are pentameric protein complexes composed of four subunits in the ratio of two alpha subunits to one beta, one epsilon, and one delta subunit. The acetylcholine receptor changes subunit composition shortly after birth when the epsilon subunit replaces the gamma subunit seen in embryonic receptors. Mutations in the epsilon subunit are associated with congenital myasthenic syndrome. [provided by RefSeq, Sep 2009]

MINK1 (HGNC:17565): (misshapen like kinase 1) This gene encodes a serine/threonine kinase belonging to the germinal center kinase (GCK) family. The protein is structurally similar to the kinases that are related to NIK and may belong to a distinct subfamily of NIK-related kinases within the GCK family. Studies of the mouse homolog indicate an up-regulation of expression in the course of postnatal mouse cerebral development and activation of the cJun N-terminal kinase (JNK) and the p38 pathways. [provided by RefSeq, Mar 2016]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 17-4897868-C-A is Benign according to our data. Variant chr17-4897868-C-A is described in ClinVar as [Benign]. Clinvar id is 323948.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-4897868-C-A is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHRNE	NM_000080.4	c.*868G>T		3_prime_UTR_variant	12/12	ENST00000649488.2
MINK1	NM_153827.5	c.*581C>A		3_prime_UTR_variant	32/32	ENST00000355280.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MINK1	ENST00000355280.11	c.*581C>A		3_prime_UTR_variant	32/32	1	NM_153827.5	A1
CHRNE	ENST00000649488.2	c.*868G>T		3_prime_UTR_variant	12/12		NM_000080.4	P1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 55168 AN: 148516 Hom.: 10439 Cov.: 25

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.407

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.356

GnomAD4 exome AF: 0.316 AC: 173 AN: 548 Hom.: 37 Cov.: 0 AF XY: 0.281 AC XY: 86 AN XY: 306

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 SAS exome AF: 0.594

Gnomad4 FIN exome AF: 0.401

Gnomad4 NFE exome AF: 0.225

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.372 AC: 55225 AN: 148634 Hom.: 10451 Cov.: 25 AF XY: 0.381 AC XY: 27596 AN XY: 72364

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.353

Alfa AF: 0.304 Hom.: 2250

Asia WGS AF: 0.563 AC: 1956 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Congenital myasthenic syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.042
Dann	Benign	0.33
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs7774; hg19: chr17-4801163; COSMIC: COSV53418092; COSMIC: COSV53418092;