9-71279169-C-T

Position:

• chr9-71279169-C-T

Variant summary

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

The NM_001366141.2(TRPM3):​c.183+167484G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 151,992 control chromosomes in the GnomAD database, including 5,653 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 0.25 (5653 hom., cov: 31)
• Consequence: TRPM3 NM_001366141.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

Genes affected

TRPM3 (HGNC:):

TRPM3 (HGNC:17992): (transient receptor potential cation channel subfamily M member 3) The product of this gene belongs to the family of transient receptor potential (TRP) channels. TRP channels are cation-selective channels important for cellular calcium signaling and homeostasis. The protein encoded by this gene mediates calcium entry, and this entry is potentiated by calcium store depletion. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRPM3	NM_001366141.2	c.183+167484G>A		intron_variant			NP_001353070.1
TRPM3	NM_001366142.2	c.183+167484G>A		intron_variant			NP_001353071.1
TRPM3	NM_001366143.2	c.183+167484G>A		intron_variant			NP_001353072.1
TRPM3	NM_001366144.2	c.183+167484G>A		intron_variant			NP_001353073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRPM3	ENST00000354500.6	n.252+167484G>A		intron_variant		1
TRPM3	ENST00000357533.6	c.183+167484G>A		intron_variant		5		ENSP00000350140.2

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37971 AN: 151880 Hom.: 5648 Cov.: 31

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.00635

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.250 AC: 38009 AN: 151992 Hom.: 5653 Cov.: 31 AF XY: 0.246 AC XY: 18304 AN XY: 74296

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.00637

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.192

Alfa AF: 0.200 Hom.: 2020

Bravo AF: 0.247

Asia WGS AF: 0.0940 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.6
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7021834; hg19: chr9-73894085;