rs353292

Positions:

• chr5-149428245-G-A

Variant summary

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

The ENST00000622374.1(LNPPS):​n.45C>T 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 0.349 in 152,306 control chromosomes in the GnomAD database, including 10,740 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 0.35 (10718 hom., cov: 32)
  • Exomes 𝑓: 0.41 (22 hom.)
• Consequence: LNPPS ENST00000622374.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

Genes affected

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

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CARMN	NR_105059.1	n.728-638G>A		intron_variant, non_coding_transcript_variant
CARMN	NR_105060.1	n.664-638G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LNPPS	ENST00000622374.1	n.45C>T		non_coding_transcript_exon_variant	1/2	5
CARMN	ENST00000602315.2	n.629-638G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53018 AN: 151978 Hom.: 10718 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.396

GnomAD4 exome AF: 0.414 AC: 87 AN: 210 Hom.: 22 Cov.: 0 AF XY: 0.462 AC XY: 49 AN XY: 106

Gnomad4 AMR exome AF: 0.538

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.333

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.417

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.349 AC: 53030 AN: 152096 Hom.: 10718 Cov.: 32 AF XY: 0.344 AC XY: 25562 AN XY: 74332

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.391

Alfa AF: 0.410 Hom.: 2719

Bravo AF: 0.350

Asia WGS AF: 0.245 AC: 853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs353292; hg19: chr5-148807808;