rs17796714

Variant names:

• chr5-149420526-G-A
• rs17796714
• ENST00000505340.6:n.264G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-149420526-G-A
• chr5-149420526-G-C

Variant summary

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

The ENST00000505340.6(CARMN):​n.264G>A 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 0.115 in 152,218 control chromosomes in the GnomAD database, including 1,435 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 0.11 (1434 hom., cov: 32)
  • Exomes 𝑓: 0.083 (1 hom.)
• Consequence: CARMN ENST00000505340.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505340.6. 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.280G>A		non_coding_transcript_exon	Exon 2 of 6
	CARMN	NR_105060.1		n.235-955G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CARMN	ENST00000505340.6	TSL:2	n.264G>A		non_coding_transcript_exon	Exon 2 of 6
	CARMN	ENST00000509909.5	TSL:4	n.247G>A		non_coding_transcript_exon	Exon 2 of 4
	CARMN	ENST00000523269.6	TSL:3	n.247G>A		non_coding_transcript_exon	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17482 AN: 152040 Hom.: 1436 Cov.: 32

Gnomad AFR AF: 0.0287

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.0691

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.0920

GnomAD4 exome AF: 0.0833 AC: 5 AN: 60 Hom.: 1 Cov.: 0 AF XY: 0.0952 AC XY: 4 AN XY: 42

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

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.333 AC: 2 AN: 6

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0455 AC: 2 AN: 44

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

GnomAD4 genome AF: 0.115 AC: 17497 AN: 152158 Hom.: 1434 Cov.: 32 AF XY: 0.118 AC XY: 8800 AN XY: 74370

African (AFR) AF: 0.0286 AC: 1189 AN: 41538

American (AMR) AF: 0.0851 AC: 1301 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0691 AC: 240 AN: 3472

East Asian (EAS) AF: 0.342 AC: 1765 AN: 5154

South Asian (SAS) AF: 0.0520 AC: 251 AN: 4824

European-Finnish (FIN) AF: 0.214 AC: 2266 AN: 10570

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10076 AN: 67998

Other (OTH) AF: 0.0967 AC: 204 AN: 2110

Alfa AF: 0.131 Hom.: 715

Bravo AF: 0.104

Asia WGS AF: 0.180 AC: 624 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	3.4
DANN	Benign	0.58
PhyloP100		0.30

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17796714;

hg19: chr5-148800089;