rs10509757

chr10-102993203-G-A

Variant summary

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

The NM_017649.5(CNNM2):c.1622-56504G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,958 control chromosomes in the GnomAD database, including 12,560 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 0.40 (12560 hom., cov: 31)
• Consequence: CNNM2 NM_017649.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

Genes affected

CNNM2 (HGNC:103): (cyclin and CBS domain divalent metal cation transport mediator 2) This gene encodes a member of the ancient conserved domain containing protein family. Members of this protein family contain a cyclin box motif and have structural similarity to the cyclins. The encoded protein may play an important role in magnesium homeostasis by mediating the epithelial transport and renal reabsorption of Mg2+. Mutations in this gene are associated with renal hypomagnesemia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNNM2	NM_017649.5	c.1622-56504G>A		intron_variant		ENST00000369878.9
CNNM2	NM_199076.3	c.1622-56504G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNNM2	ENST00000369878.9	c.1622-56504G>A		intron_variant		1	NM_017649.5	P4
CNNM2	ENST00000433628.2	c.1622-56504G>A		intron_variant		2		A1

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61270 AN: 151840 Hom.: 12549 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.404 AC: 61319 AN: 151958 Hom.: 12560 Cov.: 31 AF XY: 0.401 AC XY: 29797 AN XY: 74256

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.418

Alfa AF: 0.417 Hom.: 4659

Bravo AF: 0.405

Asia WGS AF: 0.427 AC: 1480 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	2.9
Dann	Benign	0.40

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: rs10509757; hg19: chr10-104752960;