ENST00000602964.1:n.7383C>T

Variant names:

• chr5-149427663-C-T
• rs353293
• ENST00000602964.1:n.7383C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000602964.1(CARMN):​n.7383C>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 0.331 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 ENST00000602964.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 16 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000602964.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARMN	NR_105059.1		n.728-1220C>T		intron	N/A
	CARMN	NR_105060.1		n.664-1220C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARMN	ENST00000602964.1	TSL:2	n.7383C>T		non_coding_transcript_exon	Exon 2 of 2
	CARMN	ENST00000505254.6	TSL:5	n.3149-210C>T		intron	N/A
	CARMN	ENST00000602315.3	TSL:5	n.657-1220C>T		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.333 AC: 2 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.382 AC: 13 AN: 34

Other (OTH) AF: 0.500 AC: 5 AN: 10

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

African (AFR) AF: 0.0917 AC: 3801 AN: 41454

American (AMR) AF: 0.453 AC: 6917 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1850 AN: 3470

East Asian (EAS) AF: 0.151 AC: 777 AN: 5140

South Asian (SAS) AF: 0.372 AC: 1788 AN: 4806

European-Finnish (FIN) AF: 0.371 AC: 3901 AN: 10524

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29937 AN: 67928

Other (OTH) AF: 0.373 AC: 785 AN: 2104

Alfa AF: 0.405 Hom.: 12700

Bravo AF: 0.330

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.79
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs353293; hg19: chr5-148807226;