NM_012125.4:c.-407-6959G>A

Variant names:

• chr15-34039581-G-A
• rs2684941
• NM_012125.4:c.-407-6959G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012125.4(CHRM5):​c.-407-6959G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,940 control chromosomes in the GnomAD database, including 21,033 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 0.49 (21033 hom., cov: 31)
• Consequence: CHRM5 NM_012125.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251
• Publications: 5 publications found

Genes affected

CHRM5 (HGNC:1954): (cholinergic receptor muscarinic 5) The muscarinic cholinergic receptors belong to a larger family of G protein-coupled receptors. The functional diversity of these receptors is defined by the binding of acetylcholine and includes cellular responses such as adenylate cyclase inhibition, phosphoinositide degeneration, and potassium channel mediation. Muscarinic receptors influence many effects of acetylcholine in the central and peripheral nervous system. The clinical implications of this receptor are unknown; however, stimulation of this receptor is known to increase cyclic AMP levels. [provided by RefSeq, Jul 2008]

AVEN (HGNC:13509): (apoptosis and caspase activation inhibitor) Involved in negative regulation of apoptotic process. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012125.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHRM5	NM_012125.4	MANE Select	c.-407-6959G>A		intron	N/A	NP_036257.1
	CHRM5	NM_001320917.2		c.-75-23062G>A		intron	N/A	NP_001307846.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHRM5	ENST00000383263.7	TSL:2 MANE Select	c.-407-6959G>A		intron	N/A	ENSP00000372750.5
	CHRM5	ENST00000557872.1	TSL:1	c.-76+21116G>A		intron	N/A	ENSP00000453745.1
	CHRM5	ENST00000560035.1	TSL:4	c.-75-23062G>A		intron	N/A	ENSP00000452742.1

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74443 AN: 151822 Hom.: 21027 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.490 AC: 74465 AN: 151940 Hom.: 21033 Cov.: 31 AF XY: 0.488 AC XY: 36234 AN XY: 74236

African (AFR) AF: 0.197 AC: 8171 AN: 41438

American (AMR) AF: 0.551 AC: 8416 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1603 AN: 3468

East Asian (EAS) AF: 0.486 AC: 2497 AN: 5140

South Asian (SAS) AF: 0.545 AC: 2619 AN: 4808

European-Finnish (FIN) AF: 0.557 AC: 5863 AN: 10532

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43542 AN: 67976

Other (OTH) AF: 0.527 AC: 1110 AN: 2108

Alfa AF: 0.561 Hom.: 11065

Bravo AF: 0.473

Asia WGS AF: 0.535 AC: 1862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.66
PhyloP100		-0.25
PromoterAI		-0.032	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2684941; hg19: chr15-34331782;