rs353293

Positions:

• chr5-149427663-C-T

Variant summary

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

The NR_105059.1(CARMN):​n.728-1220C>T 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 0.331 in 151,962 control chromosomes in the GnomAD database, including 10,294 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 0.33 (10289 hom., cov: 32)
  • Exomes 𝑓: 0.41 (5 hom.)
• Consequence: CARMN NR_105059.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

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]

LNPPS (HGNC:51665): (lncRNA PDCD5 and p53 scaffold)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CARMN	NR_105059.1	n.728-1220C>T		intron_variant, non_coding_transcript_variant
CARMN	NR_105060.1	n.664-1220C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CARMN	ENST00000602315.2	n.629-1220C>T		intron_variant, non_coding_transcript_variant		5
LNPPS	ENST00000622374.1	n.306+321G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50215 AN: 151788 Hom.: 10290 Cov.: 32

Gnomad AFR AF: 0.0918

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.377

GnomAD4 exome AF: 0.407 AC: 22 AN: 54 Hom.: 5 Cov.: 0 AF XY: 0.370 AC XY: 17 AN XY: 46

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.382

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.331 AC: 50221 AN: 151908 Hom.: 10289 Cov.: 32 AF XY: 0.327 AC XY: 24263 AN XY: 74222

Gnomad4 AFR AF: 0.0917

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.373

Alfa AF: 0.428 Hom.: 8684

Bravo AF: 0.330

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs353293; hg19: chr5-148807226;