rs55945735

chr5-149429595-A-Gchr5-149429595-A-T

Variant summary

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

The NR_105059.1(CARMN):n.884+556A>G 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 0.278 in 152,100 control chromosomes in the GnomAD database, including 7,369 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 0.28 (7369 hom., cov: 32)
• Consequence: CARMN NR_105059.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.643

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CARMN	NR_105059.1	n.884+556A>G		intron_variant, non_coding_transcript_variant
CARMN	NR_105060.1	n.820+556A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CARMN	ENST00000602315.2	n.785+556A>G		intron_variant, non_coding_transcript_variant		5
CARMN	ENST00000656891.1	n.634+556A>G		intron_variant, non_coding_transcript_variant
CARMN	ENST00000686037.1	n.787+556A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42289 AN: 151982 Hom.: 7375 Cov.: 32

Gnomad AFR AF: 0.0897

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.0183

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.322

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.278 AC: 42286 AN: 152100 Hom.: 7369 Cov.: 32 AF XY: 0.273 AC XY: 20264 AN XY: 74360

Gnomad4 AFR AF: 0.0897

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.0185

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.318

Alfa AF: 0.183 Hom.: 419

Bravo AF: 0.273

Asia WGS AF: 0.155 AC: 539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.8
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55945735; hg19: chr5-148809158;