rs1001555

Positions:

• chr15-31981463-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000636603.1(CHRNA7):​c.-132+14897A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,092 control chromosomes in the GnomAD database, including 1,031 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 0.11 (1031 hom., cov: 32)
• Consequence: CHRNA7 ENST00000636603.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.417

Genes affected

CHRNA7 (HGNC:1960): (cholinergic receptor nicotinic alpha 7 subunit) The nicotinic acetylcholine receptors (nAChRs) are members of a superfamily of ligand-gated ion channels that mediate fast signal transmission at synapses. The nAChRs are thought to be hetero-pentamers composed of homologous subunits. The proposed structure for each subunit is a conserved N-terminal extracellular domain followed by three conserved transmembrane domains, a variable cytoplasmic loop, a fourth conserved transmembrane domain, and a short C-terminal extracellular region. The protein encoded by this gene forms a homo-oligomeric channel, displays marked permeability to calcium ions and is a major component of brain nicotinic receptors that are blocked by, and highly sensitive to, alpha-bungarotoxin. Once this receptor binds acetylcholine, it undergoes an extensive change in conformation that affects all subunits and leads to opening of an ion-conducting channel across the plasma membrane. This gene is located in a region identified as a major susceptibility locus for juvenile myoclonic epilepsy and a chromosomal location involved in the genetic transmission of schizophrenia. An evolutionarily recent partial duplication event in this region results in a hybrid containing sequence from this gene and a novel FAM7A gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHRNA7	ENST00000635978.1	c.-43+57796A>G		intron_variant		5		ENSP00000490778
CHRNA7	ENST00000636603.1	c.-132+14897A>G		intron_variant		5		ENSP00000490513
CHRNA7	ENST00000637183.1	c.-43+3269A>G		intron_variant		5		ENSP00000490365
CHRNA7	ENST00000638106.1	c.-379+14897A>G		intron_variant		5		ENSP00000490413

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16005 AN: 151974 Hom.: 1025 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.0922

Gnomad FIN AF: 0.0318

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.0689

Gnomad OTH AF: 0.113

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.105 AC: 16033 AN: 152092 Hom.: 1031 Cov.: 32 AF XY: 0.107 AC XY: 7955 AN XY: 74378

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.0929

Gnomad4 FIN AF: 0.0318

Gnomad4 NFE AF: 0.0689

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0752 Hom.: 439

Bravo AF: 0.117

Asia WGS AF: 0.168 AC: 585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1001555; hg19: chr15-32273666;