Genetic Variant ENST00000602315.3:n.1082T>C (chr5-149431183-T-C) – 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.1082T>C 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 0.357 in 152,368 control chromosomes in the GnomAD database, including 10,329 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 0.36 ( 10307 hom., cov: 33)

Exomes 𝑓: 0.35 ( 22 hom. )

Consequence

CARMN
ENST00000602315.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

Publications

28 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=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CARMN	NR_105059.1 link	n.885-1535T>C		intron_variant	Intron 5 of 5
CARMN	NR_105060.1 link	n.821-1535T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CARMN	ENST00000602315.3 link	n.1082T>C	non_coding_transcript_exon_variant	Exon 5 of 5	5
CARMN	ENST00000656891.1 link	n.*56T>C	downstream_gene_variant
CARMN	ENST00000686037.2 link	n.*64T>C	downstream_gene_variant
CARMN	ENST00000850349.1 link	n.*56T>C	downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.358

AC:

54367

AN:

152028

Hom.:

10302

Cov.:

show subpopulations

Gnomad AFR

AF:

0.239

Gnomad AMI

AF:

0.462

Gnomad AMR

AF:

0.346

Gnomad ASJ

AF:

0.266

Gnomad EAS

AF:

0.432

Gnomad SAS

AF:

0.496

Gnomad FIN

AF:

0.354

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.422

Gnomad OTH

AF:

0.330

GnomAD4 exome

AF:

0.347

AC:

AN:

222

Hom.:

Cov.:

AF XY:

0.397

AC XY:

AN XY:

116

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.304

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)

AF:

0.667

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.387

AC:

AN:

142

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.531

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:

0.357

AC:

54387

AN:

152146

Hom.:

10307

Cov.:

AF XY:

0.358

AC XY:

26603

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.239

AC:

9912

AN:

41512

American (AMR)

AF:

0.346

AC:

5293

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.266

AC:

924

AN:

3468

East Asian (EAS)

AF:

0.432

AC:

2236

AN:

5180

South Asian (SAS)

AF:

0.497

AC:

2398

AN:

4826

European-Finnish (FIN)

AF:

0.354

AC:

3740

AN:

10570

Middle Eastern (MID)

AF:

0.269

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.422

AC:

28683

AN:

67986

Other (OTH)

AF:

0.332

AC:

701

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1765

3530

5296

7061

8826

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

552

1104

1656

2208

2760

<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:

0.391

Hom.:

37992

Bravo

AF:

0.345

Asia WGS

AF:

0.472

AC:

1640

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.22

(source)

DANN

Benign

0.40

PhyloP100

-1.1

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