rs7861254

chr9-70809868-C-T

Variant summary

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

The NM_001366145.2(TRPM3):c.973+17979G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 483,696 control chromosomes in the GnomAD database, including 18,318 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 0.31 (8507 hom., cov: 31)
  • Exomes 𝑓: 0.24 (9811 hom.)
• Consequence: TRPM3 NM_001366145.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPM3	NM_001366145.2	c.973+17979G>A		intron_variant		ENST00000677713.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPM3	ENST00000677713.2	c.973+17979G>A		intron_variant			NM_001366145.2	P4

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46489 AN: 151838 Hom.: 8495 Cov.: 31

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.298

GnomAD4 exome AF: 0.235 AC: 77989 AN: 331740 Hom.: 9811 AF XY: 0.235 AC XY: 43633 AN XY: 185922

Gnomad4 AFR exome AF: 0.503

Gnomad4 AMR exome AF: 0.201

Gnomad4 ASJ exome AF: 0.273

Gnomad4 EAS exome AF: 0.148

Gnomad4 SAS exome AF: 0.238

Gnomad4 FIN exome AF: 0.188

Gnomad4 NFE exome AF: 0.236

Gnomad4 OTH exome AF: 0.247

GnomAD4 genome AF: 0.306 AC: 46537 AN: 151956 Hom.: 8507 Cov.: 31 AF XY: 0.300 AC XY: 22317 AN XY: 74290

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.300

Alfa AF: 0.271 Hom.: 803

Bravo AF: 0.320

Asia WGS AF: 0.208 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.0020
Dann	Benign	0.16

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: rs7861254; hg19: chr9-73424784; COSMIC: COSV62474544; COSMIC: COSV62474544;