rs353291

Positions:

• chr5-149431183-T-C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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 (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	n.885-1535T>C		intron_variant, non_coding_transcript_variant
CARMN	NR_105060.1	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	n.1054T>C		non_coding_transcript_exon_variant	5/5	5

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54367 AN: 152028 Hom.: 10302 Cov.: 33

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: 77 AN: 222 Hom.: 22 Cov.: 0 AF XY: 0.397 AC XY: 46 AN XY: 116

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.: 33 AF XY: 0.358 AC XY: 26603 AN XY: 74388

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

Other links and lift over

dbSNP: rs353291; hg19: chr5-148810746;