9-70979198-C-T

Position:

• chr9-70979198-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.178-114687G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 152,054 control chromosomes in the GnomAD database, including 34,364 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 0.67 (34364 hom., cov: 31)
• Consequence: TRPM3 NM_001366145.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614

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 (SAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPM3	NM_001366145.2	c.178-114687G>A		intron_variant		ENST00000677713.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPM3	ENST00000677713.2	c.178-114687G>A		intron_variant			NM_001366145.2	P4

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101859 AN: 151934 Hom.: 34337 Cov.: 31

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.670 AC: 101929 AN: 152054 Hom.: 34364 Cov.: 31 AF XY: 0.671 AC XY: 49847 AN XY: 74314

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.665

Alfa AF: 0.695 Hom.: 15812

Bravo AF: 0.662

Asia WGS AF: 0.686 AC: 2389 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	0.78
DANN	Benign	0.74

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: rs2909295; hg19: chr9-73594114; COSMIC: COSV62665310;