Variant rs7210231 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000747.3(CHRNB1):c.1044+25C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 1,587,778 control chromosomes in the GnomAD database, including 35,146 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 3186 hom., cov: 30)

Exomes 𝑓: 0.21 ( 31960 hom. )

Consequence

CHRNB1
NM_000747.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.20

Variant links:

Genes affected

CHRNB1 (HGNC:1961): (cholinergic receptor nicotinic beta 1 subunit) The muscle acetylcholine receptor is composed of five subunits: two alpha subunits and one beta, one gamma, and one delta subunit. This gene encodes the beta subunit of the acetylcholine receptor. The acetylcholine receptor changes conformation upon acetylcholine binding leading to the opening of an ion-conducting channel across the plasma membrane. Mutations in this gene are associated with slow-channel congenital myasthenic syndrome. [provided by RefSeq, Jul 2008]

CHRNB1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BP6

Variant 17-7454545-C-A is Benign according to our data. Variant chr17-7454545-C-A is described in ClinVar as [Benign]. Clinvar id is 256771.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHRNB1	NM_000747.3 linkuse as main transcript	c.1044+25C>A		intron_variant		ENST00000306071.7	NP_000738.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHRNB1	ENST00000306071.7 linkuse as main transcript	c.1044+25C>A		intron_variant		1	NM_000747.3	ENSP00000304290	P1	P11230-1

Frequencies

GnomAD3 genomes

AF:

0.199

AC:

30186

AN:

151950

Hom.:

3191

Cov.:

show subpopulations

Gnomad AFR

AF:

0.219

Gnomad AMI

AF:

0.286

Gnomad AMR

AF:

0.154

Gnomad ASJ

AF:

0.224

Gnomad EAS

AF:

0.0360

Gnomad SAS

AF:

0.278

Gnomad FIN

AF:

0.168

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.205

Gnomad OTH

AF:

0.211

GnomAD3 exomes

AF:

0.192

AC:

48042

AN:

250578

Hom.:

5162

AF XY:

0.200

AC XY:

27078

AN XY:

135462

show subpopulations

Gnomad AFR exome

AF:

0.220

Gnomad AMR exome

AF:

0.110

Gnomad ASJ exome

AF:

0.229

Gnomad EAS exome

AF:

0.0401

Gnomad SAS exome

AF:

0.280

Gnomad FIN exome

AF:

0.178

Gnomad NFE exome

AF:

0.212

Gnomad OTH exome

AF:

0.197

GnomAD4 exome

AF:

0.206

AC:

295078

AN:

1435710

Hom.:

31960

Cov.:

AF XY:

0.208

AC XY:

148654

AN XY:

715810

show subpopulations

Gnomad4 AFR exome

AF:

0.217

Gnomad4 AMR exome

AF:

0.118

Gnomad4 ASJ exome

AF:

0.228

Gnomad4 EAS exome

AF:

0.0529

Gnomad4 SAS exome

AF:

0.273

Gnomad4 FIN exome

AF:

0.181

Gnomad4 NFE exome

AF:

0.209

Gnomad4 OTH exome

AF:

0.206

GnomAD4 genome

AF:

0.199

AC:

30189

AN:

152068

Hom.:

3186

Cov.:

AF XY:

0.196

AC XY:

14584

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.218

Gnomad4 AMR

AF:

0.153

Gnomad4 ASJ

AF:

0.224

Gnomad4 EAS

AF:

0.0361

Gnomad4 SAS

AF:

0.278

Gnomad4 FIN

AF:

0.168

Gnomad4 NFE

AF:

0.205

Gnomad4 OTH

AF:

0.208

Alfa

AF:

0.162

Hom.:

530

Bravo

AF:

0.198

Asia WGS

AF:

0.148

AC:

516

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 07, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

6.4

DANN

Benign

0.78

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over