9-71301156-T-G

Variant summary

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

The ENST00000354500.6(TRPM3):n.252+145497A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,924 control chromosomes in the GnomAD database, including 17,222 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 0.47 (17222 hom., cov: 31)
• Consequence: TRPM3 ENST00000354500.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90

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]

LOC107987079 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987079	XR_001746718.1	n.1260-18133A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPM3	ENST00000354500.6	n.252+145497A>C		intron_variant, non_coding_transcript_variant		1
TRPM3	ENST00000357533.6	c.183+145497A>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71359 AN: 151806 Hom.: 17215 Cov.: 31

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.470 AC: 71407 AN: 151924 Hom.: 17222 Cov.: 31 AF XY: 0.469 AC XY: 34833 AN XY: 74256

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.479

Alfa AF: 0.439 Hom.: 10103

Bravo AF: 0.477

Asia WGS AF: 0.540 AC: 1877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.0050
Dann	Benign	0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1566838; hg19: chr9-73916072;