rs7867868

chr9-74831958-C-T

Variant summary

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

The NM_017662.5(TRPM6):c.669+2040G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,926 control chromosomes in the GnomAD database, including 7,291 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 0.30 (7291 hom., cov: 32)
• Consequence: TRPM6 NM_017662.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

Genes affected

TRPM6 (HGNC:17995): (transient receptor potential cation channel subfamily M member 6) This gene is predominantly expressed in the kidney and colon, and encodes a protein containing an ion channel domain and a protein kinase domain. It is crucial for magnesium homeostasis, and plays an essential role in epithelial magnesium transport and in the active magnesium absorption in the gut and kidney. Mutations in this gene are associated with hypomagnesemia with secondary hypocalcemia. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Apr 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPM6	NM_017662.5	c.669+2040G>A		intron_variant		ENST00000360774.6
TRPM6	NM_001177310.2	c.654+2040G>A		intron_variant
TRPM6	NM_001177311.2	c.654+2040G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPM6	ENST00000360774.6	c.669+2040G>A		intron_variant		1	NM_017662.5	P4

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45476 AN: 151808 Hom.: 7296 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.0121

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.299 AC: 45468 AN: 151926 Hom.: 7291 Cov.: 32 AF XY: 0.293 AC XY: 21780 AN XY: 74246

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.0122

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.334

Alfa AF: 0.343 Hom.: 12297

Bravo AF: 0.295

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	8.0
Dann	Benign	0.74

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: rs7867868; hg19: chr9-77446874;