chr5-149426373-A-G

Position:

• chr5-149426373-A-G

Variant summary

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

The NR_105059.1(CARMN):​n.727+1976A>G 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 0.13 in 152,128 control chromosomes in the GnomAD database, including 1,579 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 0.13 (1579 hom., cov: 32)
  • Exomes 𝑓: 0.11 (0 hom.)
• Consequence: CARMN NR_105059.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.75

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CARMN	NR_105059.1	n.727+1976A>G		intron_variant, non_coding_transcript_variant
CARMN	NR_105060.1	n.663+1976A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CARMN	ENST00000602315.2	n.628+1976A>G		intron_variant, non_coding_transcript_variant		5
LNPPS	ENST00000622374.1	n.307-487T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19830 AN: 151964 Hom.: 1581 Cov.: 32

Gnomad AFR AF: 0.0675

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0768

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.0886

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.124

GnomAD4 exome AF: 0.109 AC: 5 AN: 46 Hom.: 0 Cov.: 0 AF XY: 0.111 AC XY: 4 AN XY: 36

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.105

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.130 AC: 19846 AN: 152082 Hom.: 1579 Cov.: 32 AF XY: 0.134 AC XY: 9987 AN XY: 74348

Gnomad4 AFR AF: 0.0676

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.0768

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.0884

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.129

Alfa AF: 0.134 Hom.: 190

Bravo AF: 0.120

Asia WGS AF: 0.199 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.087
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4705341; hg19: chr5-148805936;