chr5-149427138-A-T

Variant names:

• chr5-149427138-A-T
• rs17796757
• ENST00000602964.1:n.6858A>T

Variant summary

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

The ENST00000602964.1(CARMN):​n.6858A>T 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 0.13 in 152,078 control chromosomes in the GnomAD database, including 1,566 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 0.13 (1565 hom., cov: 31)
  • Exomes 𝑓: 0.091 (1 hom.)
• Consequence: CARMN ENST00000602964.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 8 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]

LNPPS (HGNC:51665): (lncRNA PDCD5 and p53 scaffold)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000602964.1. 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.728-1745A>T		intron	N/A
	CARMN	NR_105060.1		n.664-1745A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARMN	ENST00000602964.1	TSL:2	n.6858A>T		non_coding_transcript_exon	Exon 2 of 2
	CARMN	ENST00000505254.6	TSL:5	n.3149-735A>T		intron	N/A
	CARMN	ENST00000602315.3	TSL:5	n.657-1745A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19679 AN: 151936 Hom.: 1566 Cov.: 31

Gnomad AFR AF: 0.0669

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.0861

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.123

GnomAD4 exome AF: 0.0909 AC: 2 AN: 22 Hom.: 1 Cov.: 0 AF XY: 0.0909 AC XY: 2 AN XY: 22

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 16

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.130 AC: 19696 AN: 152056 Hom.: 1565 Cov.: 31 AF XY: 0.134 AC XY: 9928 AN XY: 74336

African (AFR) AF: 0.0670 AC: 2781 AN: 41484

American (AMR) AF: 0.107 AC: 1636 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0767 AC: 266 AN: 3468

East Asian (EAS) AF: 0.325 AC: 1676 AN: 5158

South Asian (SAS) AF: 0.0859 AC: 414 AN: 4818

European-Finnish (FIN) AF: 0.219 AC: 2319 AN: 10576

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10114 AN: 67972

Other (OTH) AF: 0.129 AC: 271 AN: 2108

Alfa AF: 0.128 Hom.: 180

Bravo AF: 0.119

Asia WGS AF: 0.199 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.7
DANN	Benign	0.83
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs17796757; hg19: chr5-148806701;