dbSNP rs17796714: CARMN:n.264G>A (chr5-149420526-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 ENST00000505340.6(CARMN):n.264G>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 0.115 in 152,218 control chromosomes in the GnomAD database, including 1,435 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 0.11 ( 1434 hom., cov: 32)

Exomes 𝑓: 0.083 ( 1 hom. )

Consequence

CARMN
ENST00000505340.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.299

Publications

4 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 (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CARMN	NR_105059.1 link	n.280G>A		non_coding_transcript_exon_variant	Exon 2 of 6
CARMN	NR_105060.1 link	n.235-955G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CARMN	ENST00000505340.6 link	n.264G>A	non_coding_transcript_exon_variant	Exon 2 of 6	2
CARMN	ENST00000509909.5 link	n.247G>A	non_coding_transcript_exon_variant	Exon 2 of 4	4
CARMN	ENST00000523269.6 link	n.247G>A	non_coding_transcript_exon_variant	Exon 2 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.115

AC:

17482

AN:

152040

Hom.:

1436

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0287

Gnomad AMI

AF:

0.202

Gnomad AMR

AF:

0.0849

Gnomad ASJ

AF:

0.0691

Gnomad EAS

AF:

0.342

Gnomad SAS

AF:

0.0516

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.148

Gnomad OTH

AF:

0.0920

GnomAD4 exome

AF:

0.0833

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0952

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.333

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0455

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.408

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.115

AC:

17497

AN:

152158

Hom.:

1434

Cov.:

AF XY:

0.118

AC XY:

8800

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.0286

AC:

1189

AN:

41538

American (AMR)

AF:

0.0851

AC:

1301

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0691

AC:

240

AN:

3472

East Asian (EAS)

AF:

0.342

AC:

1765

AN:

5154

South Asian (SAS)

AF:

0.0520

AC:

251

AN:

4824

European-Finnish (FIN)

AF:

0.214

AC:

2266

AN:

10570

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.148

AC:

10076

AN:

67998

Other (OTH)

AF:

0.0967

AC:

204

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

778

1556

2335

3113

3891

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

392

588

784

980

<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:

0.131

Hom.:

715

Bravo

AF:

0.104

Asia WGS

AF:

0.180

AC:

624

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

3.4

(source)

DANN

Benign

0.58

PhyloP100

0.30

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