rs800347

chr11-2409367-G-Achr11-2409367-G-C

Variant summary

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

The NM_014555.4(TRPM5):c.2783-1455C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,892 control chromosomes in the GnomAD database, including 28,872 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 0.61 (28872 hom., cov: 31)
• Consequence: TRPM5 NM_014555.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.669

Genes affected

TRPM5 (HGNC:14323): (transient receptor potential cation channel subfamily M member 5) This gene encodes a member of the transient receptor potential (TRP) protein family, which is a diverse group of proteins with structural features typical of ion channels. This protein plays an important role in taste transduction, and has characteristics of a calcium-activated, non-selective cation channel that carries Na+, K+, and Cs+ ions equally well, but not Ca(2+) ions. It is activated by lower concentrations of intracellular Ca(2+), and inhibited by higher concentrations. It is also a highly temperature-sensitive, heat activated channel showing a steep increase of inward currents at temperatures between 15 and 35 degrees Celsius. This gene is located within the Beckwith-Wiedemann syndrome critical region-1 on chromosome 11p15.5, and has been shown to be imprinted, with exclusive expression from the paternal allele. [provided by RefSeq, Oct 2010]

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 (AFR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPM5	NM_014555.4	c.2783-1455C>T		intron_variant		ENST00000696290.1
TRPM5	XM_017017628.2	c.2837-1455C>T		intron_variant
TRPM5	XM_047426858.1	c.2837-1455C>T		intron_variant
TRPM5	XM_047426859.1	c.1634-1455C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPM5	ENST00000696290.1	c.2783-1455C>T		intron_variant			NM_014555.4	P2
TRPM5	ENST00000528453.1	c.2783-1455C>T		intron_variant		1		A2
TRPM5	ENST00000533060.5	c.2783-1455C>T		intron_variant		1		A2
TRPM5	ENST00000533881.5	c.2765-1455C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92044 AN: 151772 Hom.: 28845 Cov.: 31

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.606 AC: 92120 AN: 151892 Hom.: 28872 Cov.: 31 AF XY: 0.604 AC XY: 44834 AN XY: 74236

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.604

Alfa AF: 0.551 Hom.: 7431

Bravo AF: 0.604

Asia WGS AF: 0.471 AC: 1643 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	2.3
Dann	Benign	0.64

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: rs800347; hg19: chr11-2430597;