dbSNP rs4705341: CARMN:n.3127A>G (chr5-149426373-A-G) – 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.3127A>G 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 0.13 in 152,128 control chromosomes in the GnomAD database, including 1,579 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 0.13 ( 1579 hom., cov: 32)

Exomes 𝑓: 0.11 ( 0 hom. )

Consequence

CARMN
ENST00000505254.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.75

Publications

10 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=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CARMN	NR_105059.1 link	n.727+1976A>G		intron_variant	Intron 4 of 5
CARMN	NR_105060.1 link	n.663+1976A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CARMN	ENST00000505254.6 link	n.3127A>G	non_coding_transcript_exon_variant	Exon 5 of 6	5
CARMN	ENST00000602964.1 link	n.6093A>G	non_coding_transcript_exon_variant	Exon 2 of 2	2
CARMN	ENST00000602315.3 link	n.656+1976A>G	intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19830

AN:

151964

Hom.:

1581

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0675

Gnomad AMI

AF:

0.200

Gnomad AMR

AF:

0.109

Gnomad ASJ

AF:

0.0768

Gnomad EAS

AF:

0.327

Gnomad SAS

AF:

0.0886

Gnomad FIN

AF:

0.219

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.150

Gnomad OTH

AF:

0.124

GnomAD4 exome

AF:

0.109

AC:

AN:

Hom.:

Cov.:

AF XY:

0.111

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.105

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.130

AC:

19846

AN:

152082

Hom.:

1579

Cov.:

AF XY:

0.134

AC XY:

9987

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.0676

AC:

2805

AN:

41482

American (AMR)

AF:

0.109

AC:

1663

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0768

AC:

266

AN:

3462

East Asian (EAS)

AF:

0.326

AC:

1680

AN:

5154

South Asian (SAS)

AF:

0.0884

AC:

426

AN:

4818

European-Finnish (FIN)

AF:

0.219

AC:

2312

AN:

10576

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.150

AC:

10201

AN:

67992

Other (OTH)

AF:

0.129

AC:

274

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

902

1803

2705

3606

4508

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

220

440

660

880

1100

<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:

0.134

Hom.:

190

Bravo

AF:

0.120

Asia WGS

AF:

0.199

AC:

692

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.087

(source)

DANN

Benign

0.55

PhyloP100

-3.8

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over