dbSNP rs3733845: CARMN:n.1837G>A (chr5-149425083-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 ENST00000505254.6(CARMN):n.1837G>A 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 0.0951 in 152,028 control chromosomes in the GnomAD database, including 954 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 0.095 ( 954 hom., cov: 32)

Exomes 𝑓: 0.077 ( 0 hom. )

Consequence

CARMN
ENST00000505254.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.91

Publications

15 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:

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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CARMN	NR_105059.1 link	n.727+686G>A		intron_variant	Intron 4 of 5
CARMN	NR_105060.1 link	n.663+686G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CARMN	ENST00000505254.6 link	n.1837G>A	non_coding_transcript_exon_variant	Exon 5 of 6	5
CARMN	ENST00000602964.1 link	n.4803G>A	non_coding_transcript_exon_variant	Exon 2 of 2	2
CARMN	ENST00000692133.1 link	n.1317G>A	non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0951

AC:

14448

AN:

151884

Hom.:

953

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0240

Gnomad AMI

AF:

0.195

Gnomad AMR

AF:

0.0811

Gnomad ASJ

AF:

0.0603

Gnomad EAS

AF:

0.278

Gnomad SAS

AF:

0.0476

Gnomad FIN

AF:

0.156

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.0822

GnomAD4 exome

AF:

0.0769

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0625

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.0714

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

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:

0.0951

AC:

14457

AN:

152002

Hom.:

954

Cov.:

AF XY:

0.0971

AC XY:

7214

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.0240

AC:

994

AN:

41486

American (AMR)

AF:

0.0809

AC:

1234

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.0603

AC:

209

AN:

3464

East Asian (EAS)

AF:

0.278

AC:

1434

AN:

5156

South Asian (SAS)

AF:

0.0479

AC:

230

AN:

4802

European-Finnish (FIN)

AF:

0.156

AC:

1646

AN:

10554

Middle Eastern (MID)

AF:

0.0884

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.122

AC:

8319

AN:

67964

Other (OTH)

AF:

0.0885

AC:

187

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

635

1270

1905

2540

3175

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

328

492

656

820

<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:

0.105

Hom.:

759

Bravo

AF:

0.0876

Asia WGS

AF:

0.157

AC:

544

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.053

(source)

DANN

Benign

0.78

PhyloP100

-2.9

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