rs11190062

Variant names:

• chr10-99345245-A-G
• rs11190062
• NM_020348.3:c.1574-12267A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000356713.5(CNNM1):​c.1574-12267A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.841 in 152,208 control chromosomes in the GnomAD database, including 54,125 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 0.84 (54125 hom., cov: 32)
• Consequence: CNNM1 ENST00000356713.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454
• Publications: 4 publications found

Genes affected

CNNM1 (HGNC:102): (cyclin and CBS domain divalent metal cation transport mediator 1) This gene encodes a member of the ancient conserved domain protein family. The encoded protein may bind copper. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000356713.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNNM1	NM_020348.3	MANE Select	c.1574-12267A>G		intron	N/A	NP_065081.2
	CNNM1	NM_001345887.2		c.1574-12267A>G		intron	N/A	NP_001332816.1
	CNNM1	NM_001345889.2		c.1574-12267A>G		intron	N/A	NP_001332818.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNNM1	ENST00000356713.5	TSL:1 MANE Select	c.1574-12267A>G		intron	N/A	ENSP00000349147.4
	CNNM1	ENST00000696687.1		c.1574-12267A>G		intron	N/A	ENSP00000512809.1

Frequencies

GnomAD3 genomes AF: 0.841 AC: 127921 AN: 152090 Hom.: 54072 Cov.: 32

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.841 AC: 128034 AN: 152208 Hom.: 54125 Cov.: 32 AF XY: 0.841 AC XY: 62566 AN XY: 74414

African (AFR) AF: 0.902 AC: 37488 AN: 41546

American (AMR) AF: 0.757 AC: 11564 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2743 AN: 3472

East Asian (EAS) AF: 0.870 AC: 4504 AN: 5178

South Asian (SAS) AF: 0.896 AC: 4319 AN: 4820

European-Finnish (FIN) AF: 0.825 AC: 8728 AN: 10584

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55975 AN: 68002

Other (OTH) AF: 0.832 AC: 1758 AN: 2114

Alfa AF: 0.826 Hom.: 9284

Bravo AF: 0.836

Asia WGS AF: 0.865 AC: 3010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.2
DANN	Benign	0.80
PhyloP100		-0.45
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: rs11190062; hg19: chr10-101105002;