chr5-149425059-T-C

Variant names:

• chr5-149425059-T-C
• rs3733846
• ENST00000505254.6:n.1813T>C

Variant summary

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

The ENST00000505254.6(CARMN):​n.1813T>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 0.184 in 152,032 control chromosomes in the GnomAD database, including 2,904 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 0.18 (2904 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CARMN ENST00000505254.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 12 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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+662T>C		intron	N/A
	CARMN	NR_105060.1		n.663+662T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARMN	ENST00000505254.6	TSL:5	n.1813T>C		non_coding_transcript_exon	Exon 5 of 6
	CARMN	ENST00000509909.5	TSL:4	n.1356T>C		non_coding_transcript_exon	Exon 4 of 4
	CARMN	ENST00000602964.1	TSL:2	n.4779T>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.184 AC: 28002 AN: 151914 Hom.: 2898 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0779

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.0880

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.165

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

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: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.184 AC: 28049 AN: 152032 Hom.: 2904 Cov.: 32 AF XY: 0.187 AC XY: 13907 AN XY: 74308

African (AFR) AF: 0.257 AC: 10648 AN: 41430

American (AMR) AF: 0.129 AC: 1964 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0779 AC: 270 AN: 3468

East Asian (EAS) AF: 0.324 AC: 1669 AN: 5152

South Asian (SAS) AF: 0.0879 AC: 424 AN: 4824

European-Finnish (FIN) AF: 0.218 AC: 2310 AN: 10576

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10180 AN: 67994

Other (OTH) AF: 0.170 AC: 359 AN: 2110

Alfa AF: 0.147 Hom.: 1003

Bravo AF: 0.183

Asia WGS AF: 0.219 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.33
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs3733846; hg19: chr5-148804622;