5-149425059-T-C

Position:

• chr5-149425059-T-C

Variant summary

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

The ENST00000602964.1(CARMN):​n.4779T>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 0.184 in 152,032 control chromosomes in the GnomAD database, including 2,904 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 0.18 (2904 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CARMN ENST00000602964.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

CARMN (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CARMN	NR_105059.1	n.727+662T>C		intron_variant
CARMN	NR_105060.1	n.663+662T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CARMN	ENST00000505254.6	n.1813T>C		non_coding_transcript_exon_variant	5/6	5
CARMN	ENST00000602964.1	n.4779T>C		non_coding_transcript_exon_variant	2/2	2
CARMN	ENST00000692133.1	n.1293T>C		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.184 AC: 28002 AN: 151914 Hom.: 2898 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0779

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.0880

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.165

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.184 AC: 28049 AN: 152032 Hom.: 2904 Cov.: 32 AF XY: 0.187 AC XY: 13907 AN XY: 74308

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.0779

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.0879

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.170

Alfa AF: 0.147 Hom.: 900

Bravo AF: 0.183

Asia WGS AF: 0.219 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3733846; hg19: chr5-148804622;