15-34057604-T-C

Position:

• chr15-34057604-T-C

Variant summary

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

The NM_012125.4(CHRM5):​c.-75-5039T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 151,952 control chromosomes in the GnomAD database, including 32,296 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 0.63 (32296 hom., cov: 31)
• Consequence: CHRM5 NM_012125.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHRM5	NM_012125.4	c.-75-5039T>C		intron_variant		ENST00000383263.7	NP_036257.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHRM5	ENST00000383263.7	c.-75-5039T>C		intron_variant		2	NM_012125.4	ENSP00000372750	P1
CHRM5	ENST00000557872.1	c.-75-5039T>C		intron_variant		1		ENSP00000453745	P1
CHRM5	ENST00000560035.1	c.-75-5039T>C		intron_variant		4		ENSP00000452742
AVEN	ENST00000675287.1	n.1637+5318A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96297 AN: 151832 Hom.: 32291 Cov.: 31

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.634 AC: 96336 AN: 151952 Hom.: 32296 Cov.: 31 AF XY: 0.632 AC XY: 46955 AN XY: 74262

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.657

Alfa AF: 0.711 Hom.: 14034

Bravo AF: 0.618

Asia WGS AF: 0.721 AC: 2509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.9
DANN	Benign	0.91

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

Other links and lift over

dbSNP: rs554303; hg19: chr15-34349805;