Variant rs2074234 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_014555.4(TRPM5):c.2508A>G(p.Thr836Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 1,612,378 control chromosomes in the GnomAD database, including 100,061 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 0.33 ( 8702 hom., cov: 33)

Exomes 𝑓: 0.35 ( 91359 hom. )

Consequence

TRPM5
NM_014555.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -7.71

Variant links:

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]

TRPM5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP7

Synonymous conserved (PhyloP=-7.71 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRPM5	NM_014555.4 linkuse as main transcript	c.2508A>G	p.Thr836Thr	synonymous_variant	22/29	ENST00000696290.1	NP_055370.1	Q9NZQ8-1
TRPM5	XM_017017628.2 linkuse as main transcript	c.2562A>G	p.Thr854Thr	synonymous_variant	19/26		XP_016873117.1
TRPM5	XM_047426858.1 linkuse as main transcript	c.2562A>G	p.Thr854Thr	synonymous_variant	19/26		XP_047282814.1
TRPM5	XM_047426859.1 linkuse as main transcript	c.1359A>G	p.Thr453Thr	synonymous_variant	10/17		XP_047282815.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TRPM5	ENST00000696290.1 linkuse as main transcript	c.2508A>G	p.Thr836Thr	synonymous_variant	22/29		NM_014555.4	ENSP00000512529.1	Q9NZQ8-1
TRPM5	ENST00000533060.5 linkuse as main transcript	c.2508A>G	p.Thr836Thr	synonymous_variant	17/24	1		ENSP00000434121.1	E9PRW0
TRPM5	ENST00000528453.1 linkuse as main transcript	c.2508A>G	p.Thr836Thr	synonymous_variant	17/24	1		ENSP00000436809.1	E9PQF7
TRPM5	ENST00000533881.5 linkuse as main transcript	c.2490A>G	p.Thr830Thr	synonymous_variant	17/24	1		ENSP00000434383.1	A0A0C4DGF4

Frequencies

GnomAD3 genomes

AF:

0.330

AC:

50163

AN:

151904

Hom.:

8698

Cov.:

show subpopulations

Gnomad AFR

AF:

0.238

Gnomad AMI

AF:

0.192

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.358

Gnomad EAS

AF:

0.430

Gnomad SAS

AF:

0.324

Gnomad FIN

AF:

0.318

Gnomad MID

AF:

0.434

Gnomad NFE

AF:

0.355

Gnomad OTH

AF:

0.375

GnomAD3 exomes

AF:

0.362

AC:

90490

AN:

249662

Hom.:

16901

AF XY:

0.362

AC XY:

49105

AN XY:

135468

show subpopulations

Gnomad AFR exome

AF:

0.235

Gnomad AMR exome

AF:

0.463

Gnomad ASJ exome

AF:

0.360

Gnomad EAS exome

AF:

0.420

Gnomad SAS exome

AF:

0.335

Gnomad FIN exome

AF:

0.317

Gnomad NFE exome

AF:

0.356

Gnomad OTH exome

AF:

0.375

GnomAD4 exome

AF:

0.351

AC:

512547

AN:

1460356

Hom.:

91359

Cov.:

AF XY:

0.351

AC XY:

254659

AN XY:

726474

show subpopulations

Gnomad4 AFR exome

AF:

0.235

Gnomad4 AMR exome

AF:

0.452

Gnomad4 ASJ exome

AF:

0.357

Gnomad4 EAS exome

AF:

0.442

Gnomad4 SAS exome

AF:

0.338

Gnomad4 FIN exome

AF:

0.316

Gnomad4 NFE exome

AF:

0.349

Gnomad4 OTH exome

AF:

0.357

GnomAD4 genome

AF:

0.330

AC:

50189

AN:

152022

Hom.:

8702

Cov.:

AF XY:

0.333

AC XY:

24781

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.238

Gnomad4 AMR

AF:

0.439

Gnomad4 ASJ

AF:

0.358

Gnomad4 EAS

AF:

0.429

Gnomad4 SAS

AF:

0.326

Gnomad4 FIN

AF:

0.318

Gnomad4 NFE

AF:

0.355

Gnomad4 OTH

AF:

0.377

Alfa

AF:

0.357

Hom.:

13477

Bravo

AF:

0.334

Asia WGS

AF:

0.357

AC:

1241

AN:

3478

EpiCase

AF:

0.367

EpiControl

AF:

0.372

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.14

DANN

Benign

0.61

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over