rs2899462

chr15-50647057-C-Achr15-50647057-C-Gchr15-50647057-C-T

Variant summary

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

The NM_017672.6(TRPM7):c.321+1630G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 152,134 control chromosomes in the GnomAD database, including 10,041 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 (10041 hom., cov: 32)
• Consequence: TRPM7 NM_017672.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290

Genes affected

TRPM7 (HGNC:17994): (transient receptor potential cation channel subfamily M member 7) This gene belongs to the melastatin subfamily of transient receptor potential family of ion channels. The protein encoded by this gene is both an ion channel and a serine/threonine protein kinase. The kinase activity is essential for the ion channel function, which serves to increase intracellular calcium levels and to help regulate magnesium ion homeostasis. The encoded protein is involved in cytoskeletal organization, cell adhesion, cell migration and organogenesis. Defects in this gene are a cause of amyotrophic lateral sclerosis-parkinsonism/dementia complex of Guam. The gene may also be associated with defects of cardiac function. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPM7	NM_017672.6	c.321+1630G>T		intron_variant		ENST00000646667.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPM7	ENST00000646667.1	c.321+1630G>T		intron_variant			NM_017672.6	A1
TRPM7	ENST00000560955.5	c.321+1630G>T		intron_variant		1		P4

Frequencies

GnomAD3 genomes AF: 0.329 AC: 50022 AN: 152016 Hom.: 10044 Cov.: 32

Gnomad AFR AF: 0.0903

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.329 AC: 50028 AN: 152134 Hom.: 10041 Cov.: 32 AF XY: 0.335 AC XY: 24928 AN XY: 74368

Gnomad4 AFR AF: 0.0903

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.390

Alfa AF: 0.221 Hom.: 545

Bravo AF: 0.327

Asia WGS AF: 0.349 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	1.2
Dann	Benign	0.60

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: rs2899462; hg19: chr15-50939254;