9-74791089-A-G

Position:

• chr9-74791089-A-G

Variant summary

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

The NM_017662.5(TRPM6):​c.2538+1535T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 152,092 control chromosomes in the GnomAD database, including 19,614 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 0.50 (19614 hom., cov: 32)
• Consequence: TRPM6 NM_017662.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRPM6	NM_017662.5	c.2538+1535T>C		intron_variant		ENST00000360774.6	NP_060132.3
TRPM6	NM_001177310.2	c.2523+1535T>C		intron_variant			NP_001170781.1
TRPM6	NM_001177311.2	c.2523+1535T>C		intron_variant			NP_001170782.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRPM6	ENST00000360774.6	c.2538+1535T>C		intron_variant		1	NM_017662.5	ENSP00000354006.1
TRPM6	ENST00000361255.7	c.2523+1535T>C		intron_variant		1		ENSP00000354962.3
TRPM6	ENST00000449912.6	c.2523+1535T>C		intron_variant		1		ENSP00000396672.2

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76588 AN: 151974 Hom.: 19570 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.504 AC: 76698 AN: 152092 Hom.: 19614 Cov.: 32 AF XY: 0.506 AC XY: 37603 AN XY: 74334

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.471

Alfa AF: 0.480 Hom.: 4431

Bravo AF: 0.511

Asia WGS AF: 0.614 AC: 2133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.78

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: rs2151423; hg19: chr9-77406005;