rs11142517

chr9-70629264-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.1633-3747G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 116,070 control chromosomes in the GnomAD database, including 14,057 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 0.46 (14057 hom., cov: 16)
• Consequence: TRPM3 NM_001366145.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPM3	NM_001366145.2	c.1633-3747G>A		intron_variant		ENST00000677713.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPM3	ENST00000677713.2	c.1633-3747G>A		intron_variant			NM_001366145.2	P4

Frequencies

GnomAD3 genomes AF: 0.464 AC: 53780 AN: 115996 Hom.: 14051 Cov.: 16

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.464 AC: 53804 AN: 116070 Hom.: 14057 Cov.: 16 AF XY: 0.463 AC XY: 24777 AN XY: 53570

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.495

Alfa AF: 0.512 Hom.: 2645

Bravo AF: 0.436

Asia WGS AF: 0.428 AC: 1482 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	6.3
Dann	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11142517; hg19: chr9-73244180;