dbSNP rs353293: CARMN:n.7383C>T (chr5-149427663-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000602964.1(CARMN):n.7383C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 151,962 control chromosomes in the GnomAD database, including 10,294 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 ( 10289 hom., cov: 32)

Exomes 𝑓: 0.41 ( 5 hom. )

Consequence

CARMN
ENST00000602964.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.57

Publications

16 publications found

Variant links:

Genes affected

CARMN (HGNC:42872): (cardiac mesoderm enhancer-associated non-coding RNA) Predicted to be involved in regulation of gene expression. [provided by Alliance of Genome Resources, Apr 2022]

CARMN links:

LNPPS (HGNC:51665): (lncRNA PDCD5 and p53 scaffold)

LNPPS links:

Genome browser will be placed here

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=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CARMN	NR_105059.1 link	n.728-1220C>T		intron_variant	Intron 4 of 5
CARMN	NR_105060.1 link	n.664-1220C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CARMN	ENST00000602964.1 link	n.7383C>T	non_coding_transcript_exon_variant	Exon 2 of 2	2
CARMN	ENST00000505254.6 link	n.3149-210C>T	intron_variant	Intron 5 of 5	5
CARMN	ENST00000602315.3 link	n.657-1220C>T	intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.331

AC:

50215

AN:

151788

Hom.:

10290

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0918

Gnomad AMI

AF:

0.370

Gnomad AMR

AF:

0.452

Gnomad ASJ

AF:

0.533

Gnomad EAS

AF:

0.151

Gnomad SAS

AF:

0.372

Gnomad FIN

AF:

0.371

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.441

Gnomad OTH

AF:

0.377

GnomAD4 exome

AF:

0.407

AC:

AN:

Hom.:

Cov.:

AF XY:

0.370

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.333

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.382

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.331

AC:

50221

AN:

151908

Hom.:

10289

Cov.:

AF XY:

0.327

AC XY:

24263

AN XY:

74222

show subpopulations

African (AFR)

AF:

0.0917

AC:

3801

AN:

41454

American (AMR)

AF:

0.453

AC:

6917

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.533

AC:

1850

AN:

3470

East Asian (EAS)

AF:

0.151

AC:

777

AN:

5140

South Asian (SAS)

AF:

0.372

AC:

1788

AN:

4806

European-Finnish (FIN)

AF:

0.371

AC:

3901

AN:

10524

Middle Eastern (MID)

AF:

0.439

AC:

129

AN:

294

European-Non Finnish (NFE)

AF:

0.441

AC:

29937

AN:

67928

Other (OTH)

AF:

0.373

AC:

785

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1523

3046

4570

6093

7616

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

494

988

1482

1976

2470

<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:

0.405

Hom.:

12700

Bravo

AF:

0.330

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.1

(source)

DANN

Benign

0.79

PhyloP100

-1.6

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over