dbSNP rs1044393: CHRNA4:p.Asp213Asp (chr20-63350772-A-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000744.7(CHRNA4):c.639T>C(p.Asp213Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.862 in 1,613,240 control chromosomes in the GnomAD database, including 604,517 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.78 ( 47932 hom., cov: 28)

Exomes 𝑓: 0.87 ( 556585 hom. )

Consequence

CHRNA4
NM_000744.7 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:11

Conservation

PhyloP100: -0.395

Publications

31 publications found

Variant links:

Genes affected

CHRNA4 (HGNC:1958): (cholinergic receptor nicotinic alpha 4 subunit) This gene encodes a nicotinic acetylcholine receptor, which belongs to a superfamily of ligand-gated ion channels that play a role in fast signal transmission at synapses. These pentameric receptors can bind acetylcholine, which causes an extensive change in conformation that leads to the opening of an ion-conducting channel across the plasma membrane. This protein is an integral membrane receptor subunit that can interact with either nAChR beta-2 or nAChR beta-4 to form a functional receptor. Mutations in this gene cause nocturnal frontal lobe epilepsy type 1. Polymorphisms in this gene that provide protection against nicotine addiction have been described. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2012]

CHRNA4 Gene-Disease associations (from GenCC):

autosomal dominant nocturnal frontal lobe epilepsy 1
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
familial sleep-related hypermotor epilepsy
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
autosomal dominant nocturnal frontal lobe epilepsy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

CHRNA4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 20-63350772-A-G is Benign according to our data. Variant chr20-63350772-A-G is described in ClinVar as Benign. ClinVar VariationId is 128749.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.395 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000744.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CHRNA4	NM_000744.7	MANE Select	c.639T>C	p.Asp213Asp	synonymous	Exon 5 of 6	NP_000735.1	P43681-1
CHRNA4	NM_001256573.2		c.111T>C	p.Asp37Asp	synonymous	Exon 5 of 6	NP_001243502.1	Q4VAQ3
CHRNA4	NR_046317.2		n.848T>C		non_coding_transcript_exon	Exon 5 of 6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CHRNA4	ENST00000370263.9	TSL:1 MANE Select	c.639T>C	p.Asp213Asp	synonymous	Exon 5 of 6	ENSP00000359285.4	P43681-1
CHRNA4	ENST00000463705.5	TSL:1	n.1287T>C		non_coding_transcript_exon	Exon 4 of 5
CHRNA4	ENST00000467563.3	TSL:1	n.709T>C		non_coding_transcript_exon	Exon 5 of 6

Frequencies

GnomAD3 genomes

AF:

0.781

AC:

118258

AN:

151408

Hom.:

47914

Cov.:

show subpopulations

Gnomad AFR

AF:

0.539

Gnomad AMI

AF:

0.914

Gnomad AMR

AF:

0.861

Gnomad ASJ

AF:

0.836

Gnomad EAS

AF:

0.870

Gnomad SAS

AF:

0.785

Gnomad FIN

AF:

0.894

Gnomad MID

AF:

0.756

Gnomad NFE

AF:

0.881

Gnomad OTH

AF:

0.788

GnomAD2 exomes

AF:

0.846

AC:

212327

AN:

251030

AF XY:

0.847

show subpopulations

Gnomad AFR exome

AF:

0.527

Gnomad AMR exome

AF:

0.914

Gnomad ASJ exome

AF:

0.827

Gnomad EAS exome

AF:

0.868

Gnomad FIN exome

AF:

0.889

Gnomad NFE exome

AF:

0.878

Gnomad OTH exome

AF:

0.847

GnomAD4 exome

AF:

0.870

AC:

1271958

AN:

1461714

Hom.:

556585

Cov.:

AF XY:

0.869

AC XY:

631585

AN XY:

727142

show subpopulations

African (AFR)

AF:

0.519

AC:

17381

AN:

33480

American (AMR)

AF:

0.908

AC:

40595

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.824

AC:

21543

AN:

26136

East Asian (EAS)

AF:

0.877

AC:

34814

AN:

39700

South Asian (SAS)

AF:

0.786

AC:

67813

AN:

86258

European-Finnish (FIN)

AF:

0.889

AC:

47340

AN:

53248

Middle Eastern (MID)

AF:

0.760

AC:

4384

AN:

5768

European-Non Finnish (NFE)

AF:

0.887

AC:

986644

AN:

1112006

Other (OTH)

AF:

0.852

AC:

51444

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

12288

24577

36865

49154

61442

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21322

42644

63966

85288

106610

<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:

0.781

AC:

118314

AN:

151526

Hom.:

47932

Cov.:

AF XY:

0.785

AC XY:

58109

AN XY:

73998

show subpopulations

African (AFR)

AF:

0.538

AC:

22192

AN:

41232

American (AMR)

AF:

0.861

AC:

13125

AN:

15238

Ashkenazi Jewish (ASJ)

AF:

0.836

AC:

2899

AN:

3468

East Asian (EAS)

AF:

0.869

AC:

4420

AN:

5086

South Asian (SAS)

AF:

0.786

AC:

3748

AN:

4770

European-Finnish (FIN)

AF:

0.894

AC:

9414

AN:

10534

Middle Eastern (MID)

AF:

0.752

AC:

221

AN:

294

European-Non Finnish (NFE)

AF:

0.881

AC:

59802

AN:

67894

Other (OTH)

AF:

0.791

AC:

1659

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1077

2154

3230

4307

5384

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

844

1688

2532

3376

4220

<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:

0.774

Hom.:

22267

Bravo

AF:

0.769

Asia WGS

AF:

0.811

AC:

2821

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (5)

not provided (3)

Autosomal dominant nocturnal frontal lobe epilepsy (1)

Autosomal dominant nocturnal frontal lobe epilepsy 1 (1)

Inborn genetic diseases (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.48

(source)

DANN

Benign

0.58

PhyloP100

-0.40

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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