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. Variant got -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

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]

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPM3	NM_001366145.2	c.3708-5095C>T		intron_variant	Intron 25 of 25	ENST00000677713.2	NP_001353074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPM3	ENST00000677713.2	c.3708-5095C>T		intron_variant	Intron 25 of 25		NM_001366145.2	ENSP00000503830.2

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

Gnomad4 AFR AF: 0.874

Gnomad4 AMR AF: 0.886

Gnomad4 ASJ AF: 0.879

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.859

Gnomad4 NFE AF: 0.858

Gnomad4 OTH AF: 0.870

Alfa AF: 0.857 Hom.: 13163

Bravo AF: 0.877

Asia WGS AF: 0.833 AC: 2895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.029
DANN	Benign	0.20

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: rs10780944; hg19: chr9-73157416;