dbSNP rs41291957: CARMN:n.657-56G>A (chr5-149428827-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 ENST00000602315.3(CARMN):n.657-56G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 457,350 control chromosomes in the GnomAD database, including 4,704 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 0.12 ( 1556 hom., cov: 32)

Exomes 𝑓: 0.13 ( 3148 hom. )

Consequence

CARMN
ENST00000602315.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0550

Publications

31 publications found

Variant links:

COSMIC-nc: COSV66047168

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:

MIR143 (HGNC:31530): (microRNA 143) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR143 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
CARMN	NR_105059.1 link	n.728-56G>A	intron_variant	Intron 4 of 5
CARMN	NR_105060.1 link	n.664-56G>A	intron_variant	Intron 3 of 4
MIR143	NR_029684.1 link	n.-91G>A	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CARMN	ENST00000602315.3 link	n.657-56G>A	intron_variant	Intron 3 of 4	5
CARMN	ENST00000656891.1 link	n.478-56G>A	intron_variant	Intron 3 of 4
CARMN	ENST00000686037.2 link	n.631-56G>A	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.119

AC:

18146

AN:

152108

Hom.:

1556

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0290

Gnomad AMI

AF:

0.310

Gnomad AMR

AF:

0.0888

Gnomad ASJ

AF:

0.0845

Gnomad EAS

AF:

0.311

Gnomad SAS

AF:

0.0685

Gnomad FIN

AF:

0.269

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.147

Gnomad OTH

AF:

0.0950

GnomAD4 exome

AF:

0.128

AC:

39185

AN:

305122

Hom.:

3148

Cov.:

AF XY:

0.123

AC XY:

21202

AN XY:

172984

show subpopulations

African (AFR)

AF:

0.0273

AC:

230

AN:

8422

American (AMR)

AF:

0.0865

AC:

2278

AN:

26322

Ashkenazi Jewish (ASJ)

AF:

0.0814

AC:

838

AN:

10300

East Asian (EAS)

AF:

0.308

AC:

2776

AN:

9008

South Asian (SAS)

AF:

0.0628

AC:

3712

AN:

59080

European-Finnish (FIN)

AF:

0.254

AC:

5402

AN:

21254

Middle Eastern (MID)

AF:

0.0549

AC:

AN:

1440

European-Non Finnish (NFE)

AF:

0.142

AC:

22080

AN:

155496

Other (OTH)

AF:

0.130

AC:

1790

AN:

13800

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1622

3244

4865

6487

8109

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

140

280

420

560

700

<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:

0.119

AC:

18155

AN:

152228

Hom.:

1556

Cov.:

AF XY:

0.126

AC XY:

9349

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.0289

AC:

1202

AN:

41556

American (AMR)

AF:

0.0885

AC:

1354

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0845

AC:

293

AN:

3468

East Asian (EAS)

AF:

0.310

AC:

1602

AN:

5166

South Asian (SAS)

AF:

0.0688

AC:

332

AN:

4828

European-Finnish (FIN)

AF:

0.269

AC:

2844

AN:

10584

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.147

AC:

10005

AN:

68004

Other (OTH)

AF:

0.102

AC:

216

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

762

1524

2286

3048

3810

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

200

400

600

800

1000

<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:

0.130

Hom.:

513

Bravo

AF:

0.104

Asia WGS

AF:

0.191

AC:

664

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.5

(source)

DANN

Benign

0.33

PhyloP100

-0.055

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