rs10780944

Variant names:

• chr9-70542500-G-A
• rs10780944
• NM_001366145.2:c.3708-5095C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-70542500-G-A
• chr9-70542500-G-C
• chr9-70542500-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001366145.2(TRPM3):​c.3708-5095C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.865 in 152,186 control chromosomes in the GnomAD database, including 57,027 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 0.86 (57027 hom., cov: 31)
• Consequence: TRPM3 NM_001366145.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 7 publications found

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]

ENSG00000308298 (HGNC:):

KLF9-DT (HGNC:54815): (KLF9 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366145.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPM3	NM_001366145.2	MANE Select	c.3708-5095C>T		intron	N/A	NP_001353074.1	Q9HCF6-3
	TRPM3	NM_001366147.2		c.3783-5095C>T		intron	N/A	NP_001353076.1
	TRPM3	NM_001366141.2		c.3678-5095C>T		intron	N/A	NP_001353070.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPM3	ENST00000677713.2	MANE Select	c.3708-5095C>T		intron	N/A	ENSP00000503830.2	Q9HCF6-3
	TRPM3	ENST00000377110.9	TSL:1	c.3672-5095C>T		intron	N/A	ENSP00000366314.4	Q9HCF6-2
	TRPM3	ENST00000377111.8	TSL:1	c.3672-5095C>T		intron	N/A	ENSP00000366315.4	Q9HCF6-10

Frequencies

GnomAD3 genomes AF: 0.865 AC: 131487 AN: 152068 Hom.: 56972 Cov.: 31

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.865 AC: 131602 AN: 152186 Hom.: 57027 Cov.: 31 AF XY: 0.862 AC XY: 64139 AN XY: 74390

African (AFR) AF: 0.874 AC: 36307 AN: 41520

American (AMR) AF: 0.886 AC: 13564 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3049 AN: 3470

East Asian (EAS) AF: 0.973 AC: 5018 AN: 5158

South Asian (SAS) AF: 0.694 AC: 3347 AN: 4822

European-Finnish (FIN) AF: 0.859 AC: 9101 AN: 10592

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.858 AC: 58339 AN: 68006

Other (OTH) AF: 0.870 AC: 1836 AN: 2110

Alfa AF: 0.867 Hom.: 109821

Bravo AF: 0.877

Asia WGS AF: 0.833 AC: 2895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.029
DANN	Benign	0.20
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10780944; hg19: chr9-73157416;