rs4744628

chr9-71316862-G-Achr9-71316862-G-C

Variant summary

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

The ENST00000354500.6(TRPM3):n.252+129791C>T 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 0.705 in 152,024 control chromosomes in the GnomAD database, including 40,248 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 0.71 (40248 hom., cov: 32)
• Consequence: TRPM3 ENST00000354500.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987079	XR_001746718.1	n.1259+10098C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPM3	ENST00000354500.6	n.252+129791C>T		intron_variant, non_coding_transcript_variant		1
TRPM3	ENST00000357533.6	c.183+129791C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107168 AN: 151906 Hom.: 40237 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.705 AC: 107214 AN: 152024 Hom.: 40248 Cov.: 32 AF XY: 0.709 AC XY: 52698 AN XY: 74326

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.785

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.756

Alfa AF: 0.803 Hom.: 98259

Bravo AF: 0.687

Asia WGS AF: 0.788 AC: 2741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.60
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4744628; hg19: chr9-73931778;