chr5-149425083-G-A

Variant names:

• chr5-149425083-G-A
• rs3733845
• ENST00000505254.6:n.1837G>A

Variant summary

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

The ENST00000505254.6(CARMN):​n.1837G>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 0.0951 in 152,028 control chromosomes in the GnomAD database, including 954 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 0.095 (954 hom., cov: 32)
  • Exomes 𝑓: 0.077 (0 hom.)
• Consequence: CARMN ENST00000505254.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.91
• Publications: 15 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 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.727+686G>A		intron	N/A
	CARMN	NR_105060.1		n.663+686G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARMN	ENST00000505254.6	TSL:5	n.1837G>A		non_coding_transcript_exon	Exon 5 of 6
	CARMN	ENST00000602964.1	TSL:2	n.4803G>A		non_coding_transcript_exon	Exon 2 of 2
	CARMN	ENST00000692133.1		n.1317G>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0951 AC: 14448 AN: 151884 Hom.: 953 Cov.: 32

Gnomad AFR AF: 0.0240

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.0811

Gnomad ASJ AF: 0.0603

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.0476

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0822

GnomAD4 exome AF: 0.0769 AC: 2 AN: 26 Hom.: 0 Cov.: 0 AF XY: 0.0625 AC XY: 1 AN XY: 16

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

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

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0714 AC: 1 AN: 14

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 6

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

GnomAD4 genome AF: 0.0951 AC: 14457 AN: 152002 Hom.: 954 Cov.: 32 AF XY: 0.0971 AC XY: 7214 AN XY: 74272

African (AFR) AF: 0.0240 AC: 994 AN: 41486

American (AMR) AF: 0.0809 AC: 1234 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0603 AC: 209 AN: 3464

East Asian (EAS) AF: 0.278 AC: 1434 AN: 5156

South Asian (SAS) AF: 0.0479 AC: 230 AN: 4802

European-Finnish (FIN) AF: 0.156 AC: 1646 AN: 10554

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8319 AN: 67964

Other (OTH) AF: 0.0885 AC: 187 AN: 2114

Alfa AF: 0.105 Hom.: 759

Bravo AF: 0.0876

Asia WGS AF: 0.157 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.053
DANN	Benign	0.78
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs3733845; hg19: chr5-148804646;