chr5-149426373-A-G

Variant names:

• chr5-149426373-A-G
• rs4705341
• ENST00000505254.6:n.3127A>G

Variant summary

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

The ENST00000602964.1(CARMN):​n.6093A>G 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 0.13 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 ENST00000602964.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.75
• Publications: 10 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARMN	NR_105059.1		n.727+1976A>G		intron	N/A
	CARMN	NR_105060.1		n.663+1976A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARMN	ENST00000505254.6	TSL:5	n.3127A>G		non_coding_transcript_exon	Exon 5 of 6
	CARMN	ENST00000602964.1	TSL:2	n.6093A>G		non_coding_transcript_exon	Exon 2 of 2
	CARMN	ENST00000602315.3	TSL:5	n.656+1976A>G		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

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

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.105 AC: 4 AN: 38

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.0676 AC: 2805 AN: 41482

American (AMR) AF: 0.109 AC: 1663 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0768 AC: 266 AN: 3462

East Asian (EAS) AF: 0.326 AC: 1680 AN: 5154

South Asian (SAS) AF: 0.0884 AC: 426 AN: 4818

European-Finnish (FIN) AF: 0.219 AC: 2312 AN: 10576

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10201 AN: 67992

Other (OTH) AF: 0.129 AC: 274 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.087
DANN	Benign	0.55
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs4705341; hg19: chr5-148805936;