5-149427138-A-T

Position:

• chr5-149427138-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

CARMN (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CARMN	NR_105059.1	n.728-1745A>T		intron_variant
CARMN	NR_105060.1	n.664-1745A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CARMN	ENST00000602964.1	n.6858A>T		non_coding_transcript_exon_variant	2/2	2
CARMN	ENST00000505254.6	n.3149-735A>T		intron_variant		5
CARMN	ENST00000602315.2	n.629-1745A>T		intron_variant		5

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

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.0670

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0767

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.0859

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.129

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17796757; hg19: chr5-148806701;