rs3733845

Positions:

• chr5-149425083-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000602964.1(CARMN):​n.4803G>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 0.0951 in 152,028 control chromosomes in the GnomAD database, including 954 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 0.095 (954 hom., cov: 32)
  • Exomes 𝑓: 0.077 (0 hom.)
• Consequence: CARMN ENST00000602964.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.91

Genes affected

CARMN (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CARMN	NR_105059.1	n.727+686G>A		intron_variant
CARMN	NR_105060.1	n.663+686G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CARMN	ENST00000505254.6	n.1837G>A		non_coding_transcript_exon_variant	5/6	5
CARMN	ENST00000602964.1	n.4803G>A		non_coding_transcript_exon_variant	2/2	2
CARMN	ENST00000692133.1	n.1317G>A		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.0951 AC: 14448 AN: 151884 Hom.: 953 Cov.: 32

Gnomad AFR AF: 0.0240

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.0811

Gnomad ASJ AF: 0.0603

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.0476

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0822

GnomAD4 exome AF: 0.0769 AC: 2 AN: 26 Hom.: 0 Cov.: 0 AF XY: 0.0625 AC XY: 1 AN XY: 16

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0714

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0951 AC: 14457 AN: 152002 Hom.: 954 Cov.: 32 AF XY: 0.0971 AC XY: 7214 AN XY: 74272

Gnomad4 AFR AF: 0.0240

Gnomad4 AMR AF: 0.0809

Gnomad4 ASJ AF: 0.0603

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.0479

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.0885

Alfa AF: 0.105 Hom.: 653

Bravo AF: 0.0876

Asia WGS AF: 0.157 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.053
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3733845; hg19: chr5-148804646;