NM_014555.4:c.2783-1455C>T

Variant names:

• chr11-2409367-G-A
• rs800347
• NM_014555.4:c.2783-1455C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TRPM5	NM_014555.4	c.2783-1455C>T		intron_variant	Intron 23 of 28	ENST00000696290.1	NP_055370.1
TRPM5	XM_017017628.2	c.2837-1455C>T		intron_variant	Intron 20 of 25		XP_016873117.1
TRPM5	XM_047426858.1	c.2837-1455C>T		intron_variant	Intron 20 of 25		XP_047282814.1
TRPM5	XM_047426859.1	c.1634-1455C>T		intron_variant	Intron 11 of 16		XP_047282815.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPM5	ENST00000696290.1	c.2783-1455C>T		intron_variant	Intron 23 of 28		NM_014555.4	ENSP00000512529.1
TRPM5	ENST00000533060.5	c.2783-1455C>T		intron_variant	Intron 18 of 23	1		ENSP00000434121.1
TRPM5	ENST00000528453.1	c.2783-1455C>T		intron_variant	Intron 18 of 23	1		ENSP00000436809.1
TRPM5	ENST00000533881.5	c.2765-1455C>T		intron_variant	Intron 18 of 23	1		ENSP00000434383.1

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

African (AFR) AF: 0.752 AC: 31140 AN: 41418

American (AMR) AF: 0.487 AC: 7437 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2219 AN: 3462

East Asian (EAS) AF: 0.324 AC: 1666 AN: 5142

South Asian (SAS) AF: 0.613 AC: 2948 AN: 4808

European-Finnish (FIN) AF: 0.594 AC: 6270 AN: 10550

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38378 AN: 67920

Other (OTH) AF: 0.604 AC: 1274 AN: 2110

Alfa AF: 0.574 Hom.: 46823

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
PhyloP100		-0.67
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: rs800347; hg19: chr11-2430597;