ENST00000602315.3:n.814-560G>A

Variant names:

• chr5-149430355-G-A
• rs73798217
• ENST00000602315.3:n.814-560G>A

Variant summary

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

The ENST00000602315.3(CARMN):​n.814-560G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0597 in 152,222 control chromosomes in the GnomAD database, including 767 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 0.060 (767 hom., cov: 32)
• Consequence: CARMN ENST00000602315.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 3 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000602315.3. 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.884+1316G>A		intron	N/A
	CARMN	NR_105060.1		n.820+1316G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARMN	ENST00000602315.3	TSL:5	n.814-560G>A		intron	N/A
	CARMN	ENST00000656891.1		n.635-560G>A		intron	N/A
	CARMN	ENST00000686037.2		n.788-413G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9059 AN: 152104 Hom.: 762 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0269

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0281

Gnomad FIN AF: 0.00349

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00611

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0597 AC: 9084 AN: 152222 Hom.: 767 Cov.: 32 AF XY: 0.0580 AC XY: 4313 AN XY: 74418

African (AFR) AF: 0.189 AC: 7825 AN: 41488

American (AMR) AF: 0.0269 AC: 411 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0403 AC: 140 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0280 AC: 135 AN: 4828

European-Finnish (FIN) AF: 0.00349 AC: 37 AN: 10610

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00612 AC: 416 AN: 68022

Other (OTH) AF: 0.0511 AC: 108 AN: 2114

Alfa AF: 0.0588 Hom.: 416

Bravo AF: 0.0676

Asia WGS AF: 0.0330 AC: 114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.45
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs73798217; hg19: chr5-148809918;