Variant 5-149429595-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_105059.1(CARMN):n.884+556A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,100 control chromosomes in the GnomAD database, including 7,369 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 0.28 ( 7369 hom., cov: 32)

Consequence

CARMN
NR_105059.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.643

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CARMN	NR_105059.1 linkuse as main transcript	n.884+556A>G		intron_variant, non_coding_transcript_variant
CARMN	NR_105060.1 linkuse as main transcript	n.820+556A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
CARMN	ENST00000602315.2 linkuse as main transcript	n.785+556A>G	intron_variant, non_coding_transcript_variant	5
CARMN	ENST00000656891.1 linkuse as main transcript	n.634+556A>G	intron_variant, non_coding_transcript_variant
CARMN	ENST00000686037.1 linkuse as main transcript	n.787+556A>G	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.278

AC:

42289

AN:

151982

Hom.:

7375

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0897

Gnomad AMI

AF:

0.363

Gnomad AMR

AF:

0.317

Gnomad ASJ

AF:

0.467

Gnomad EAS

AF:

0.0183

Gnomad SAS

AF:

0.325

Gnomad FIN

AF:

0.289

Gnomad MID

AF:

0.404

Gnomad NFE

AF:

0.387

Gnomad OTH

AF:

0.322

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.278

AC:

42286

AN:

152100

Hom.:

7369

Cov.:

AF XY:

0.273

AC XY:

20264

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.0897

Gnomad4 AMR

AF:

0.316

Gnomad4 ASJ

AF:

0.467

Gnomad4 EAS

AF:

0.0185

Gnomad4 SAS

AF:

0.326

Gnomad4 FIN

AF:

0.289

Gnomad4 NFE

AF:

0.387

Gnomad4 OTH

AF:

0.318

Alfa

AF:

0.183

Hom.:

419

Bravo

AF:

0.273

Asia WGS

AF:

0.155

AC:

539

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.8

DANN

Benign

0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over