rs1831144

chr9-70775125-G-Achr9-70775125-G-C

Variant summary

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

The NM_001366145.2(TRPM3):c.1148+8980C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,094 control chromosomes in the GnomAD database, including 4,464 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 0.22 (4464 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: TRPM3 NM_001366145.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.849

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPM3	NM_001366145.2	c.1148+8980C>T		intron_variant		ENST00000677713.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPM3	ENST00000677713.2	c.1148+8980C>T		intron_variant			NM_001366145.2	P4

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33219 AN: 151976 Hom.: 4469 Cov.: 32

Gnomad AFR AF: 0.0642

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.233

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: 0.218 AC: 33223 AN: 152094 Hom.: 4464 Cov.: 32 AF XY: 0.217 AC XY: 16094 AN XY: 74310

Gnomad4 AFR AF: 0.0643

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.232

Alfa AF: 0.226 Hom.: 1260

Bravo AF: 0.214

Asia WGS AF: 0.155 AC: 539 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.044
Dann	Benign	0.49

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: rs1831144; hg19: chr9-73390041;