Variant chr5-149431183-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000602315.2(CARMN):n.1054T>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
ENST00000602315.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

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=-0.82).

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/exons	MANE	Protein	UniProt
CARMN	NR_105059.1 linkuse as main transcript	n.885-1535T>C		intron_variant, non_coding_transcript_variant
CARMN	NR_105060.1 linkuse as main transcript	n.821-1535T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CARMN	ENST00000602315.2 linkuse as main transcript	n.1054T>C		non_coding_transcript_exon_variant	5/5	5

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

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.304

Gnomad4 EAS exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.667

Gnomad4 NFE exome

AF:

0.387

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.357

AC:

54387

AN:

152146

Hom.:

10307

Cov.:

AF XY:

0.358

AC XY:

26603

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.239

Gnomad4 AMR

AF:

0.346

Gnomad4 ASJ

AF:

0.266

Gnomad4 EAS

AF:

0.432

Gnomad4 SAS

AF:

0.497

Gnomad4 FIN

AF:

0.354

Gnomad4 NFE

AF:

0.422

Gnomad4 OTH

AF:

0.332

Alfa

AF:

0.400

Hom.:

25948

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

DANN

Benign

0.40

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