rs10117842

chr9-70826521-A-Cchr9-70826521-A-G

Variant summary

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

The NM_001366145.2(TRPM3):c.973+1326T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,096 control chromosomes in the GnomAD database, including 15,286 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 0.44 (15286 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: TRPM3 NM_001366145.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

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 (NFE) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPM3	NM_001366145.2	c.973+1326T>G		intron_variant		ENST00000677713.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPM3	ENST00000677713.2	c.973+1326T>G		intron_variant			NM_001366145.2	P4

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66160 AN: 151978 Hom.: 15283 Cov.: 33

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.443

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.435 AC: 66196 AN: 152096 Hom.: 15286 Cov.: 33 AF XY: 0.434 AC XY: 32286 AN XY: 74356

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.445

Alfa AF: 0.484 Hom.: 35465

Bravo AF: 0.419

Asia WGS AF: 0.275 AC: 958 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	2.7
Dann	Benign	0.65

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: rs10117842; hg19: chr9-73441437;