ENST00000505254.6:n.3794T>C

Variant names:

• chr5-149428518-T-C
• rs4705343
• ENST00000505254.6:n.3794T>C

Variant summary

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

The ENST00000505254.6(CARMN):​n.3794T>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 0.141 in 171,074 control chromosomes in the GnomAD database, including 2,102 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 0.14 (1938 hom., cov: 32)
  • Exomes 𝑓: 0.12 (164 hom.)
• Consequence: CARMN ENST00000505254.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 30 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505254.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARMN	NR_105059.1		n.728-365T>C		intron	N/A
	CARMN	NR_105060.1		n.664-365T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARMN	ENST00000505254.6	TSL:5	n.3794T>C		non_coding_transcript_exon	Exon 6 of 6
	CARMN	ENST00000602964.1	TSL:2	n.8238T>C		non_coding_transcript_exon	Exon 2 of 2
	CARMN	ENST00000602315.3	TSL:5	n.657-365T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21944 AN: 152044 Hom.: 1940 Cov.: 32

Gnomad AFR AF: 0.0692

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0920

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.130

GnomAD4 exome AF: 0.116 AC: 2188 AN: 18912 Hom.: 164 Cov.: 0 AF XY: 0.110 AC XY: 1109 AN XY: 10112

African (AFR) AF: 0.00847 AC: 1 AN: 118

American (AMR) AF: 0.0898 AC: 241 AN: 2684

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 15 AN: 286

East Asian (EAS) AF: 0.250 AC: 79 AN: 316

South Asian (SAS) AF: 0.0864 AC: 310 AN: 3588

European-Finnish (FIN) AF: 0.173 AC: 126 AN: 728

Middle Eastern (MID) AF: 0.0769 AC: 4 AN: 52

European-Non Finnish (NFE) AF: 0.128 AC: 1318 AN: 10288

Other (OTH) AF: 0.110 AC: 94 AN: 852

GnomAD4 genome AF: 0.144 AC: 21963 AN: 152162 Hom.: 1938 Cov.: 32 AF XY: 0.149 AC XY: 11113 AN XY: 74382

African (AFR) AF: 0.0693 AC: 2878 AN: 41514

American (AMR) AF: 0.114 AC: 1746 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0920 AC: 319 AN: 3466

East Asian (EAS) AF: 0.319 AC: 1651 AN: 5170

South Asian (SAS) AF: 0.109 AC: 527 AN: 4832

European-Finnish (FIN) AF: 0.258 AC: 2726 AN: 10562

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11548 AN: 68010

Other (OTH) AF: 0.137 AC: 290 AN: 2114

Alfa AF: 0.152 Hom.: 255

Bravo AF: 0.131

Asia WGS AF: 0.213 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.44
DANN	Benign	0.76
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4705343; hg19: chr5-148808081;