rs1328142

Positions:

• chr9-70783498-C-A
• chr9-70783498-C-G

Variant summary

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

The NM_001366145.2(TRPM3):​c.1148+607G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 151,930 control chromosomes in the GnomAD database, including 3,633 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 0.21 (3633 hom., cov: 31)
• Consequence: TRPM3 NM_001366145.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPM3	NM_001366145.2	c.1148+607G>T		intron_variant		ENST00000677713.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPM3	ENST00000677713.2	c.1148+607G>T		intron_variant			NM_001366145.2	P4

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31355 AN: 151812 Hom.: 3629 Cov.: 31

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.207 AC: 31392 AN: 151930 Hom.: 3633 Cov.: 31 AF XY: 0.206 AC XY: 15331 AN XY: 74244

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.199

Alfa AF: 0.175 Hom.: 538

Bravo AF: 0.218

Asia WGS AF: 0.224 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.17
DANN	Benign	0.70

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: rs1328142; hg19: chr9-73398414;