5-149431183-T-C

Variant names:

• chr5-149431183-T-C
• rs353291
• ENST00000602315.3:n.1082T>C

Variant summary

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

The ENST00000602315.3(CARMN):​n.1082T>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 0.357 in 152,368 control chromosomes in the GnomAD database, including 10,329 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 0.36 (10307 hom., cov: 33)
  • Exomes 𝑓: 0.35 (22 hom.)
• Consequence: CARMN ENST00000602315.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 28 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 (SAS) allele frequency at 95% confidence interval = 0.48 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARMN	NR_105059.1		n.885-1535T>C		intron	N/A
	CARMN	NR_105060.1		n.821-1535T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARMN	ENST00000602315.3	TSL:5	n.1082T>C		non_coding_transcript_exon	Exon 5 of 5
	CARMN	ENST00000656891.1		n.*56T>C		downstream_gene	N/A
	CARMN	ENST00000686037.2		n.*64T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54367 AN: 152028 Hom.: 10302 Cov.: 33

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.330

GnomAD4 exome AF: 0.347 AC: 77 AN: 222 Hom.: 22 Cov.: 0 AF XY: 0.397 AC XY: 46 AN XY: 116

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.304 AC: 14 AN: 46

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 2 AN: 4

South Asian (SAS) AF: 0.00 AC: 0 AN: 10

European-Finnish (FIN) AF: 0.667 AC: 4 AN: 6

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.387 AC: 55 AN: 142

Other (OTH) AF: 0.250 AC: 2 AN: 8

GnomAD4 genome AF: 0.357 AC: 54387 AN: 152146 Hom.: 10307 Cov.: 33 AF XY: 0.358 AC XY: 26603 AN XY: 74388

African (AFR) AF: 0.239 AC: 9912 AN: 41512

American (AMR) AF: 0.346 AC: 5293 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 924 AN: 3468

East Asian (EAS) AF: 0.432 AC: 2236 AN: 5180

South Asian (SAS) AF: 0.497 AC: 2398 AN: 4826

European-Finnish (FIN) AF: 0.354 AC: 3740 AN: 10570

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28683 AN: 67986

Other (OTH) AF: 0.332 AC: 701 AN: 2110

Alfa AF: 0.391 Hom.: 37992

Bravo AF: 0.345

Asia WGS AF: 0.472 AC: 1640 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	0.22
DANN	Benign	0.40
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs353291; hg19: chr5-148810746;