5-149428245-G-A

Variant names:

• chr5-149428245-G-A
• rs353292
• ENST00000505254.6:n.3521G>A

Variant summary

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

The ENST00000505254.6(CARMN):​n.3521G>A 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: CARMN ENST00000505254.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.45 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARMN	NR_105059.1		n.728-638G>A		intron	N/A
	CARMN	NR_105060.1		n.664-638G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARMN	ENST00000505254.6	TSL:5	n.3521G>A		non_coding_transcript_exon	Exon 6 of 6
	CARMN	ENST00000602964.1	TSL:2	n.7965G>A		non_coding_transcript_exon	Exon 2 of 2
	LNPPS	ENST00000622374.1	TSL:5	n.45C>T		non_coding_transcript_exon	Exon 1 of 2

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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.538 AC: 14 AN: 26

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.333 AC: 2 AN: 6

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.417 AC: 70 AN: 168

Other (OTH) AF: 0.250 AC: 1 AN: 4

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

African (AFR) AF: 0.150 AC: 6226 AN: 41508

American (AMR) AF: 0.459 AC: 7008 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1847 AN: 3468

East Asian (EAS) AF: 0.152 AC: 783 AN: 5166

South Asian (SAS) AF: 0.372 AC: 1795 AN: 4820

European-Finnish (FIN) AF: 0.382 AC: 4042 AN: 10570

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

European-Non Finnish (NFE) AF: 0.442 AC: 30037 AN: 67960

Other (OTH) AF: 0.391 AC: 827 AN: 2114

Alfa AF: 0.394 Hom.: 4598

Bravo AF: 0.350

Asia WGS AF: 0.245 AC: 853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.9
DANN	Benign	0.64
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs353292; hg19: chr5-148807808;