rs55945735

Variant names:

• chr5-149429595-A-G
• rs55945735
• ENST00000602315.3:n.813+556A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-149429595-A-G
• chr5-149429595-A-T

Variant summary

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

The ENST00000602315.3(CARMN):​n.813+556A>G variant causes a intron 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 ENST00000602315.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.643
• Publications: 4 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=-0.89).
• 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 rank	MANE	Protein	UniProt
CARMN	NR_105059.1	n.884+556A>G		intron_variant	Intron 5 of 5
CARMN	NR_105060.1	n.820+556A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CARMN	ENST00000602315.3	n.813+556A>G		intron_variant	Intron 4 of 4	5
CARMN	ENST00000656891.1	n.634+556A>G		intron_variant	Intron 4 of 4
CARMN	ENST00000686037.2	n.787+556A>G		intron_variant	Intron 4 of 4
CARMN	ENST00000850349.1	n.851+556A>G		intron_variant	Intron 5 of 5

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

African (AFR) AF: 0.0897 AC: 3725 AN: 41528

American (AMR) AF: 0.316 AC: 4834 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1617 AN: 3466

East Asian (EAS) AF: 0.0185 AC: 96 AN: 5182

South Asian (SAS) AF: 0.326 AC: 1566 AN: 4806

European-Finnish (FIN) AF: 0.289 AC: 3053 AN: 10554

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.387 AC: 26276 AN: 67966

Other (OTH) AF: 0.318 AC: 672 AN: 2110

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
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs55945735; hg19: chr5-148809158;