rs4705343

Positions:

• chr5-149428518-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_105059.1(CARMN):​n.728-365T>C variant causes a intron, non coding transcript 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 NR_105059.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CARMN	NR_105059.1	n.728-365T>C		intron_variant, non_coding_transcript_variant
CARMN	NR_105060.1	n.664-365T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CARMN	ENST00000602315.2	n.629-365T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR exome AF: 0.00847

Gnomad4 AMR exome AF: 0.0898

Gnomad4 ASJ exome AF: 0.0524

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 0.0864

Gnomad4 FIN exome AF: 0.173

Gnomad4 NFE exome AF: 0.128

Gnomad4 OTH exome AF: 0.110

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

Gnomad4 AFR AF: 0.0693

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0920

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.137

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4705343; hg19: chr5-148808081;