Genetic Variant NM_024734.4:c.*6136C>T (chr14-95185428-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024734.4(CLMN):c.*6136C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0981 in 152,338 control chromosomes in the GnomAD database, including 965 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 0.098 ( 961 hom., cov: 31)

Exomes 𝑓: 0.13 ( 4 hom. )

Consequence

CLMN
NM_024734.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0150

Publications

6 publications found

Variant links:

Genes affected

CLMN (HGNC:19972): (calmin) Predicted to enable actin filament binding activity. Predicted to be involved in negative regulation of cell population proliferation and nuclear migration. Predicted to act upstream of or within neuron projection development. Predicted to be integral component of membrane. Predicted to be part of meiotic nuclear membrane microtubule tethering complex. Predicted to be active in cytoplasm and nuclear outer membrane. [provided by Alliance of Genome Resources, Apr 2022]

CLMN links:

ENSG00000259143 (HGNC:):

ENSG00000259143 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024734.4. 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
	CLMN	NM_024734.4	MANE Select	c.*6136C>T		3_prime_UTR	Exon 13 of 13	NP_079010.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLMN	ENST00000298912.9	TSL:1 MANE Select	c.*6136C>T		3_prime_UTR	Exon 13 of 13	ENSP00000298912.3
	ENSG00000259143	ENST00000556796.1	TSL:4	n.370+57C>T		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0981

AC:

14913

AN:

152002

Hom.:

959

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0757

Gnomad AMI

AF:

0.0615

Gnomad AMR

AF:

0.0790

Gnomad ASJ

AF:

0.150

Gnomad EAS

AF:

0.347

Gnomad SAS

AF:

0.176

Gnomad FIN

AF:

0.111

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.0873

Gnomad OTH

AF:

0.103

GnomAD4 exome

AF:

0.128

AC:

AN:

218

Hom.:

Cov.:

AF XY:

0.139

AC XY:

AN XY:

158

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.333

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.122

AC:

AN:

172

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0981

AC:

14918

AN:

152120

Hom.:

961

Cov.:

AF XY:

0.103

AC XY:

7690

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.0754

AC:

3131

AN:

41506

American (AMR)

AF:

0.0794

AC:

1213

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.150

AC:

521

AN:

3472

East Asian (EAS)

AF:

0.349

AC:

1798

AN:

5158

South Asian (SAS)

AF:

0.176

AC:

846

AN:

4804

European-Finnish (FIN)

AF:

0.111

AC:

1174

AN:

10582

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0873

AC:

5935

AN:

68000

Other (OTH)

AF:

0.101

AC:

214

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

667

1334

2002

2669

3336

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

178

356

534

712

890

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0853

Hom.:

370

Bravo

AF:

0.0937

Asia WGS

AF:

0.235

AC:

813

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.3

(source)

DANN

Benign

0.54

PhyloP100

0.015

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over