Variant rs1320149 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000305510.4(CNNM3):c.1731T>C(p.Phe577=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 1,613,686 control chromosomes in the GnomAD database, including 27,264 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 0.27 ( 11713 hom., cov: 32)

Exomes 𝑓: 0.10 ( 15551 hom. )

Consequence

CNNM3
ENST00000305510.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Variant links:

Genes affected

CNNM3 (HGNC:104): (cyclin and CBS domain divalent metal cation transport mediator 3) Predicted to enable transmembrane transporter activity. Predicted to be involved in ion transport; magnesium ion homeostasis; and transmembrane transport. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

CNNM3 links:

ANKRD23 (HGNC:24470): (ankyrin repeat domain 23) This gene is a member of the muscle ankyrin repeat protein (MARP) family and encodes a protein with four tandem ankyrin-like repeats. The protein is localized to the nucleus, functioning as a transcriptional regulator. Expression of this protein is induced during recovery following starvation. [provided by RefSeq, Jul 2008]

ANKRD23 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP7

Synonymous conserved (PhyloP=-1.03 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNNM3	NM_017623.5 linkuse as main transcript	c.1731T>C	p.Phe577=	synonymous_variant	5/8	ENST00000305510.4	NP_060093.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNNM3	ENST00000305510.4 linkuse as main transcript	c.1731T>C	p.Phe577=	synonymous_variant	5/8	1	NM_017623.5	ENSP00000305449	P1	Q8NE01-1
CNNM3	ENST00000465224.5 linkuse as main transcript	n.587T>C		non_coding_transcript_exon_variant	3/4	1
CNNM3	ENST00000377060.7 linkuse as main transcript	c.1587T>C	p.Phe529=	synonymous_variant	4/7	2		ENSP00000366260		Q8NE01-2
ANKRD23	ENST00000476975.5 linkuse as main transcript	n.799-3281A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.271

AC:

41243

AN:

151926

Hom.:

11658

Cov.:

show subpopulations

Gnomad AFR

AF:

0.725

Gnomad AMI

AF:

0.0921

Gnomad AMR

AF:

0.164

Gnomad ASJ

AF:

0.147

Gnomad EAS

AF:

0.153

Gnomad SAS

AF:

0.0946

Gnomad FIN

AF:

0.0665

Gnomad MID

AF:

0.223

Gnomad NFE

AF:

0.0835

Gnomad OTH

AF:

0.247

GnomAD3 exomes

AF:

0.134

AC:

33605

AN:

251364

Hom.:

5684

AF XY:

0.122

AC XY:

16550

AN XY:

135856

show subpopulations

Gnomad AFR exome

AF:

0.745

Gnomad AMR exome

AF:

0.0918

Gnomad ASJ exome

AF:

0.146

Gnomad EAS exome

AF:

0.149

Gnomad SAS exome

AF:

0.0792

Gnomad FIN exome

AF:

0.0718

Gnomad NFE exome

AF:

0.0824

Gnomad OTH exome

AF:

0.128

GnomAD4 exome

AF:

0.0999

AC:

146007

AN:

1461642

Hom.:

15551

Cov.:

AF XY:

0.0980

AC XY:

71295

AN XY:

727134

show subpopulations

Gnomad4 AFR exome

AF:

0.755

Gnomad4 AMR exome

AF:

0.0994

Gnomad4 ASJ exome

AF:

0.149

Gnomad4 EAS exome

AF:

0.141

Gnomad4 SAS exome

AF:

0.0809

Gnomad4 FIN exome

AF:

0.0710

Gnomad4 NFE exome

AF:

0.0775

Gnomad4 OTH exome

AF:

0.145

GnomAD4 genome

AF:

0.272

AC:

41354

AN:

152044

Hom.:

11713

Cov.:

AF XY:

0.266

AC XY:

19781

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.725

Gnomad4 AMR

AF:

0.163

Gnomad4 ASJ

AF:

0.147

Gnomad4 EAS

AF:

0.153

Gnomad4 SAS

AF:

0.0953

Gnomad4 FIN

AF:

0.0665

Gnomad4 NFE

AF:

0.0834

Gnomad4 OTH

AF:

0.249

Alfa

AF:

0.162

Hom.:

3184

Bravo

AF:

0.299

Asia WGS

AF:

0.217

AC:

751

AN:

3478

EpiCase

AF:

0.0946

EpiControl

AF:

0.0883

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

2.5

DANN

Benign

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over