9-70678150-A-G

Position:

• chr9-70678150-A-G

Variant summary

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

The NM_001366145.2(TRPM3):​c.1345+3356T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 152,042 control chromosomes in the GnomAD database, including 33,172 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 0.66 (33172 hom., cov: 31)
• Consequence: TRPM3 NM_001366145.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

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]

LOC105376078 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPM3	NM_001366145.2	c.1345+3356T>C		intron_variant		ENST00000677713.2
LOC105376078	XR_007061573.1	n.4202+5263A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPM3	ENST00000677713.2	c.1345+3356T>C		intron_variant			NM_001366145.2	P4

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99696 AN: 151924 Hom.: 33139 Cov.: 31

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.656 AC: 99781 AN: 152042 Hom.: 33172 Cov.: 31 AF XY: 0.657 AC XY: 48817 AN XY: 74294

Gnomad4 AFR AF: 0.759

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.647

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.637

Alfa AF: 0.643 Hom.: 4434

Bravo AF: 0.651

Asia WGS AF: 0.691 AC: 2405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.23

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: rs1317604; hg19: chr9-73293066;