rs6819816

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017581.4(CHRNA9):​c.*243G>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 0.193 in 411,902 control chromosomes in the GnomAD database, including 9,227 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 0.17 ( 2803 hom., cov: 32)
Exomes 𝑓: 0.21 ( 6424 hom. )

Consequence

CHRNA9
NM_017581.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.865
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CHRNA9NM_017581.4 linkuse as main transcriptc.*243G>A 3_prime_UTR_variant 5/5 ENST00000310169.3 NP_060051.2 Q9UGM1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CHRNA9ENST00000310169.3 linkuse as main transcriptc.*243G>A 3_prime_UTR_variant 5/51 NM_017581.4 ENSP00000312663.2 Q9UGM1

Frequencies

GnomAD3 genomes
AF:
0.170
AC:
25854
AN:
151992
Hom.:
2805
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0443
Gnomad AMI
AF:
0.202
Gnomad AMR
AF:
0.174
Gnomad ASJ
AF:
0.133
Gnomad EAS
AF:
0.0492
Gnomad SAS
AF:
0.154
Gnomad FIN
AF:
0.249
Gnomad MID
AF:
0.239
Gnomad NFE
AF:
0.245
Gnomad OTH
AF:
0.178
GnomAD4 exome
AF:
0.207
AC:
53686
AN:
259798
Hom.:
6424
Cov.:
0
AF XY:
0.205
AC XY:
27390
AN XY:
133464
show subpopulations
Gnomad4 AFR exome
AF:
0.0423
Gnomad4 AMR exome
AF:
0.172
Gnomad4 ASJ exome
AF:
0.144
Gnomad4 EAS exome
AF:
0.0338
Gnomad4 SAS exome
AF:
0.152
Gnomad4 FIN exome
AF:
0.234
Gnomad4 NFE exome
AF:
0.247
Gnomad4 OTH exome
AF:
0.197
GnomAD4 genome
AF:
0.170
AC:
25851
AN:
152104
Hom.:
2803
Cov.:
32
AF XY:
0.170
AC XY:
12602
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.0442
Gnomad4 AMR
AF:
0.174
Gnomad4 ASJ
AF:
0.133
Gnomad4 EAS
AF:
0.0495
Gnomad4 SAS
AF:
0.155
Gnomad4 FIN
AF:
0.249
Gnomad4 NFE
AF:
0.245
Gnomad4 OTH
AF:
0.177
Alfa
AF:
0.206
Hom.:
826
Bravo
AF:
0.158
Asia WGS
AF:
0.0960
AC:
333
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
3.9
DANN
Benign
0.67

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.

Other links and lift over

dbSNP: rs6819816; hg19: chr4-40356780; COSMIC: COSV59573991; COSMIC: COSV59573991; API