ENST00000354500.6:n.252+29421A>C

Variant names:

• chr9-71417232-T-G
• rs12350232
• ENST00000354500.6:n.252+29421A>C

Variant summary

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

The ENST00000354500.6(TRPM3):​n.252+29421A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,674 control chromosomes in the GnomAD database, including 15,612 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 0.45 (15612 hom., cov: 31)
• Consequence: TRPM3 ENST00000354500.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530

Genes affected

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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPM3	NM_001366141.2	c.183+29421A>C		intron_variant	Intron 1 of 24		NP_001353070.1
TRPM3	NM_001366142.2	c.183+29421A>C		intron_variant	Intron 1 of 26		NP_001353071.1
TRPM3	NM_001366143.2	c.183+29421A>C		intron_variant	Intron 1 of 25		NP_001353072.1
TRPM3	NM_001366144.2	c.183+29421A>C		intron_variant	Intron 1 of 6		NP_001353073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPM3	ENST00000354500.6	n.252+29421A>C		intron_variant	Intron 1 of 5	1
TRPM3	ENST00000357533.6	c.183+29421A>C		intron_variant	Intron 1 of 24	5		ENSP00000350140.2

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68229 AN: 151556 Hom.: 15600 Cov.: 31

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.450 AC: 68273 AN: 151674 Hom.: 15612 Cov.: 31 AF XY: 0.453 AC XY: 33537 AN XY: 74102

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.438

Alfa AF: 0.455 Hom.: 8291

Bravo AF: 0.446

Asia WGS AF: 0.446 AC: 1548 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	6.3
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12350232; hg19: chr9-74032148;