rs17796714

chr5-149420526-G-Achr5-149420526-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_105059.1(CARMN):n.280G>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 NR_105059.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CARMN	NR_105059.1	n.280G>A		non_coding_transcript_exon_variant	2/6
CARMN	NR_105060.1	n.235-955G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CARMN	ENST00000602315.2	n.200-955G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17482 AN: 152040 Hom.: 1436 Cov.: 32

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: 5 AN: 60 Hom.: 1 Cov.: 0 AF XY: 0.0952 AC XY: 4 AN XY: 42

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.333

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.0455

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.115 AC: 17497 AN: 152158 Hom.: 1434 Cov.: 32 AF XY: 0.118 AC XY: 8800 AN XY: 74370

Gnomad4 AFR AF: 0.0286

Gnomad4 AMR AF: 0.0851

Gnomad4 ASJ AF: 0.0691

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.0520

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.0967

Alfa AF: 0.128 Hom.: 396

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
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17796714; hg19: chr5-148800089;