chr17-4901891-C-A

Variant names:

Variant summary

Our verdict is . The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001145536.2(C17orf107):c.*1358C>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 0.00482 in 1,606,316 control chromosomes in the GnomAD database, including 309 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.022 ( 135 hom., cov: 32)

Exomes 𝑓: 0.0030 ( 174 hom. )

Consequence

C17orf107
NM_001145536.2 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.668

Publications

0 publications found

Variant links:

Genes affected

C17orf107 (HGNC:37238): (chromosome 17 open reading frame 107)

C17orf107 links:

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]

CHRNE Gene-Disease associations (from GenCC):

congenital myasthenic syndrome
Inheritance: AR Classification: DEFINITIVE Submitted by: Illumina
congenital myasthenic syndrome 4A
Inheritance: AD, AR Classification: STRONG Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
congenital myasthenic syndrome 4B
Inheritance: AR Classification: STRONG Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
congenital myasthenic syndrome 4C
Inheritance: AR Classification: STRONG Submitted by: Genomics England PanelApp
postsynaptic congenital myasthenic syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

CHRNE links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_001145536.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 17-4901891-C-A is Benign according to our data. Variant chr17-4901891-C-A is described in ClinVar as Benign. ClinVar VariationId is 1222421.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0728 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145536.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C17orf107	NM_001145536.2	MANE Select	c.*1358C>A		3_prime_UTR	Exon 3 of 3	NP_001139008.1	Q6ZR85
	CHRNE	NM_000080.4	MANE Select	c.500+41G>T		intron	N/A	NP_000071.1	Q04844

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
C17orf107	ENST00000381365.4	TSL:2 MANE Select	c.*1358C>A	3_prime_UTR	Exon 3 of 3	ENSP00000370770.3	Q6ZR85
CHRNE	ENST00000649488.2	MANE Select	c.500+41G>T	intron	N/A	ENSP00000497829.1	Q04844
C17orf107	ENST00000861085.1		c.*1358C>A	3_prime_UTR	Exon 3 of 3	ENSP00000531144.1

Frequencies

GnomAD3 genomes

AF:

0.0223

AC:

3397

AN:

152032

Hom.:

136

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0750

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0109

Gnomad ASJ

AF:

0.00605

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00955

Gnomad NFE

AF:

0.000882

Gnomad OTH

AF:

0.0191

GnomAD2 exomes

AF:

0.00615

AC:

1519

AN:

247018

AF XY:

0.00454

show subpopulations

Gnomad AFR exome

AF:

0.0766

Gnomad AMR exome

AF:

0.00452

Gnomad ASJ exome

AF:

0.00449

Gnomad EAS exome

AF:

0.000493

Gnomad FIN exome

AF:

0.0000928

Gnomad NFE exome

AF:

0.000749

Gnomad OTH exome

AF:

0.00365

GnomAD4 exome

AF:

0.00298

AC:

4338

AN:

1454166

Hom.:

174

Cov.:

AF XY:

0.00266

AC XY:

1926

AN XY:

723674

show subpopulations

African (AFR)

AF:

0.0814

AC:

2669

AN:

32772

American (AMR)

AF:

0.00515

AC:

230

AN:

44668

Ashkenazi Jewish (ASJ)

AF:

0.00406

AC:

106

AN:

26090

East Asian (EAS)

AF:

0.000454

AC:

AN:

39626

South Asian (SAS)

AF:

0.00128

AC:

110

AN:

85992

European-Finnish (FIN)

AF:

0.0000377

AC:

AN:

53006

Middle Eastern (MID)

AF:

0.00530

AC:

AN:

4716

European-Non Finnish (NFE)

AF:

0.000747

AC:

827

AN:

1107334

Other (OTH)

AF:

0.00585

AC:

351

AN:

59962

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.638

Heterozygous variant carriers

146

292

438

584

730

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

104

208

312

416

520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0224

AC:

3405

AN:

152150

Hom.:

135

Cov.:

AF XY:

0.0213

AC XY:

1586

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.0750

AC:

3107

AN:

41430

American (AMR)

AF:

0.0109

AC:

167

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.00605

AC:

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5172

South Asian (SAS)

AF:

0.00124

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10620

Middle Eastern (MID)

AF:

0.0103

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.000882

AC:

AN:

68004

Other (OTH)

AF:

0.0189

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.537

Heterozygous variant carriers

154

309

463

618

772

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00333

Hom.:

Bravo

AF:

0.0254

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

6.5

(source)

DANN

Benign

0.87

PhyloP100

0.67

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over