rs1889915

Variant names:

• chr9-70549796-T-C
• rs1889915
• NM_001366145.2:c.3575-122A>G

Your query was ambiguous. Multiple possible variants found:

• chr9-70549796-T-C
• chr9-70549796-T-G

Variant summary

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

The NM_001366145.2(TRPM3):​c.3575-122A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 989,682 control chromosomes in the GnomAD database, including 120,942 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 0.49 (18741 hom., cov: 31)
  • Exomes 𝑓: 0.48 (102201 hom.)
• Consequence: TRPM3 NM_001366145.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPM3	NM_001366145.2	c.3575-122A>G		intron_variant	Intron 24 of 25	ENST00000677713.2	NP_001353074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPM3	ENST00000677713.2	c.3575-122A>G		intron_variant	Intron 24 of 25		NM_001366145.2	ENSP00000503830.2

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74295 AN: 151872 Hom.: 18740 Cov.: 31

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.495

GnomAD4 exome AF: 0.485 AC: 405998 AN: 837692 Hom.: 102201 AF XY: 0.481 AC XY: 201382 AN XY: 418534

African (AFR) AF: 0.398 AC: 7395 AN: 18586

American (AMR) AF: 0.508 AC: 8254 AN: 16256

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 7600 AN: 15012

East Asian (EAS) AF: 0.787 AC: 23617 AN: 30010

South Asian (SAS) AF: 0.339 AC: 14983 AN: 44154

European-Finnish (FIN) AF: 0.601 AC: 17987 AN: 29950

Middle Eastern (MID) AF: 0.514 AC: 2169 AN: 4216

European-Non Finnish (NFE) AF: 0.476 AC: 305547 AN: 641630

Other (OTH) AF: 0.487 AC: 18446 AN: 37878

GnomAD4 genome AF: 0.489 AC: 74323 AN: 151990 Hom.: 18741 Cov.: 31 AF XY: 0.492 AC XY: 36508 AN XY: 74260

African (AFR) AF: 0.408 AC: 16921 AN: 41452

American (AMR) AF: 0.499 AC: 7622 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1814 AN: 3470

East Asian (EAS) AF: 0.819 AC: 4233 AN: 5168

South Asian (SAS) AF: 0.342 AC: 1647 AN: 4820

European-Finnish (FIN) AF: 0.606 AC: 6378 AN: 10530

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34088 AN: 67964

Other (OTH) AF: 0.493 AC: 1042 AN: 2112

Alfa AF: 0.501 Hom.: 63810

Bravo AF: 0.488

Asia WGS AF: 0.524 AC: 1824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.64
PhyloP100		0.027
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: rs1889915; hg19: chr9-73164712;