dbSNP rs56291234: CHRNA9:c.*362C>T (chr4-40354882-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017581.4(CHRNA9):c.*362C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0905 in 179,834 control chromosomes in the GnomAD database, including 1,424 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 0.099 ( 1375 hom., cov: 32)

Exomes 𝑓: 0.044 ( 49 hom. )

Consequence

CHRNA9
NM_017581.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.549

Publications

6 publications found

Variant links:

Genes affected

CHRNA9 (HGNC:14079): (cholinergic receptor nicotinic alpha 9 subunit) This gene is a member of the ligand-gated ionic channel family and nicotinic acetylcholine receptor gene superfamily. It encodes a plasma membrane protein that forms homo- or hetero-oligomeric divalent cation channels. This protein is involved in cochlea hair cell development and is also expressed in the outer hair cells (OHCs) of the adult cochlea. [provided by RefSeq, Feb 2012]

CHRNA9 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHRNA9	NM_017581.4 link	c.*362C>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000310169.3	NP_060051.2	Q9UGM1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHRNA9	ENST00000310169.3 link	c.*362C>T		3_prime_UTR_variant	Exon 5 of 5	1	NM_017581.4	ENSP00000312663.2		Q9UGM1

Frequencies

GnomAD3 genomes

AF:

0.0987

AC:

15013

AN:

152036

Hom.:

1371

Cov.:

show subpopulations

Gnomad AFR

AF:

0.234

Gnomad AMI

AF:

0.0868

Gnomad AMR

AF:

0.0546

Gnomad ASJ

AF:

0.102

Gnomad EAS

AF:

0.00115

Gnomad SAS

AF:

0.0358

Gnomad FIN

AF:

0.0140

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0522

Gnomad OTH

AF:

0.0876

GnomAD4 exome

AF:

0.0444

AC:

1230

AN:

27680

Hom.:

Cov.:

AF XY:

0.0442

AC XY:

635

AN XY:

14378

show subpopulations

African (AFR)

AF:

0.179

AC:

139

AN:

778

American (AMR)

AF:

0.0421

AC:

142

AN:

3374

Ashkenazi Jewish (ASJ)

AF:

0.0979

AC:

AN:

664

East Asian (EAS)

AF:

0.00

AC:

AN:

2042

South Asian (SAS)

AF:

0.0390

AC:

104

AN:

2670

European-Finnish (FIN)

AF:

0.0179

AC:

AN:

840

Middle Eastern (MID)

AF:

0.0541

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0436

AC:

691

AN:

15848

Other (OTH)

AF:

0.0504

AC:

AN:

1390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

105

157

210

262

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.0989

AC:

15041

AN:

152154

Hom.:

1375

Cov.:

AF XY:

0.0957

AC XY:

7121

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.234

AC:

9695

AN:

41478

American (AMR)

AF:

0.0544

AC:

832

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.102

AC:

354

AN:

3466

East Asian (EAS)

AF:

0.00116

AC:

AN:

5188

South Asian (SAS)

AF:

0.0354

AC:

171

AN:

4826

European-Finnish (FIN)

AF:

0.0140

AC:

148

AN:

10606

Middle Eastern (MID)

AF:

0.0782

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0522

AC:

3550

AN:

67988

Other (OTH)

AF:

0.0866

AC:

183

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

622

1245

1867

2490

3112

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

312

468

624

780

<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:

0.0679

Hom.:

558

Bravo

AF:

0.109

Asia WGS

AF:

0.0370

AC:

128

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.2

(source)

DANN

Benign

0.24

PhyloP100

-0.55

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over