dbSNP rs353292: CARMN:n.3521G>A (chr5-149428245-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.3521G>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 0.349 in 152,306 control chromosomes in the GnomAD database, including 10,740 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 0.35 ( 10718 hom., cov: 32)

Exomes 𝑓: 0.41 ( 22 hom. )

Consequence

CARMN
ENST00000505254.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0950

Publications

30 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=-0.8).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CARMN	NR_105059.1 link	n.728-638G>A		intron_variant	Intron 4 of 5
CARMN	NR_105060.1 link	n.664-638G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CARMN	ENST00000505254.6 link	n.3521G>A	non_coding_transcript_exon_variant	Exon 6 of 6	5
CARMN	ENST00000602964.1 link	n.7965G>A	non_coding_transcript_exon_variant	Exon 2 of 2	2
LNPPS	ENST00000622374.1 link	n.45C>T	non_coding_transcript_exon_variant	Exon 1 of 2	5

Frequencies

GnomAD3 genomes

AF:

0.349

AC:

53018

AN:

151978

Hom.:

10718

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.368

Gnomad AMR

AF:

0.458

Gnomad ASJ

AF:

0.533

Gnomad EAS

AF:

0.151

Gnomad SAS

AF:

0.372

Gnomad FIN

AF:

0.382

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.442

Gnomad OTH

AF:

0.396

GnomAD4 exome

AF:

0.414

AC:

AN:

210

Hom.:

Cov.:

AF XY:

0.462

AC XY:

AN XY:

106

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.538

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.333

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.417

AC:

AN:

168

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.527

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.349

AC:

53030

AN:

152096

Hom.:

10718

Cov.:

AF XY:

0.344

AC XY:

25562

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.150

AC:

6226

AN:

41508

American (AMR)

AF:

0.459

AC:

7008

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.533

AC:

1847

AN:

3468

East Asian (EAS)

AF:

0.152

AC:

783

AN:

5166

South Asian (SAS)

AF:

0.372

AC:

1795

AN:

4820

European-Finnish (FIN)

AF:

0.382

AC:

4042

AN:

10570

Middle Eastern (MID)

AF:

0.439

AC:

129

AN:

294

European-Non Finnish (NFE)

AF:

0.442

AC:

30037

AN:

67960

Other (OTH)

AF:

0.391

AC:

827

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1662

3323

4985

6646

8308

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

520

1040

1560

2080

2600

<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:

0.394

Hom.:

4598

Bravo

AF:

0.350

Asia WGS

AF:

0.245

AC:

853

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.9

(source)

DANN

Benign

0.64

PhyloP100

-0.095

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