2-174772073-A-G

Variant summary

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

The ENST00000636168.2(CHRNA1):​c.-447+4032T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,986 control chromosomes in the GnomAD database, including 12,659 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 0.40 ( 12659 hom., cov: 32)

Consequence

CHRNA1
ENST00000636168.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.579
Variant links:
Genes affected
CHRNA1 (HGNC:1955): (cholinergic receptor nicotinic alpha 1 subunit) The muscle acetylcholine receptor consiststs of 5 subunits of 4 different types: 2 alpha subunits and 1 each of the beta, gamma, and delta subunits. This gene encodes an alpha subunit that plays a role in acetlycholine binding/channel gating. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Nov 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=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000236449ENST00000442996.1 linkn.322-676A>G intron_variant Intron 3 of 3 1
CHRNA1ENST00000636168.2 linkc.-447+4032T>C intron_variant Intron 2 of 9 5 ENSP00000490338.2 A0A1B0GV17
ENSG00000236449ENST00000654673.1 linkn.285A>G non_coding_transcript_exon_variant Exon 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.401
AC:
60824
AN:
151868
Hom.:
12643
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.452
Gnomad AMI
AF:
0.164
Gnomad AMR
AF:
0.423
Gnomad ASJ
AF:
0.272
Gnomad EAS
AF:
0.684
Gnomad SAS
AF:
0.455
Gnomad FIN
AF:
0.412
Gnomad MID
AF:
0.329
Gnomad NFE
AF:
0.348
Gnomad OTH
AF:
0.370
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.401
AC:
60883
AN:
151986
Hom.:
12659
Cov.:
32
AF XY:
0.408
AC XY:
30318
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.453
Gnomad4 AMR
AF:
0.423
Gnomad4 ASJ
AF:
0.272
Gnomad4 EAS
AF:
0.684
Gnomad4 SAS
AF:
0.455
Gnomad4 FIN
AF:
0.412
Gnomad4 NFE
AF:
0.348
Gnomad4 OTH
AF:
0.370
Alfa
AF:
0.345
Hom.:
11506
Bravo
AF:
0.404
Asia WGS
AF:
0.541
AC:
1885
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
7.7
DANN
Benign
0.66

Splicing

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: rs935863; hg19: chr2-175636801; API