5-71720635-CA-C

Position:

• chr5-71720635-CA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_004291.4(CARTPT):​c.*21delA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.097 in 1,552,968 control chromosomes in the GnomAD database, including 8,136 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.081 (623 hom., cov: 31)
  • Exomes 𝑓: 0.099 (7513 hom.)
• Consequence: CARTPT NM_004291.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.371

Genes affected

CARTPT (HGNC:24323): (CART prepropeptide) This gene encodes a preproprotein that is proteolytically processed to generate multiple biologically active peptides. These peptides play a role in appetite, energy balance, maintenance of body weight, reward and addiction, and the stress response. Expression of a similar gene transcript in rodents is upregulated following administration of cocaine and amphetamine. Mutations in this gene are associated with susceptibility to obesity in humans. [provided by RefSeq, Feb 2016]

CARTPT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 5-71720635-CA-C is Benign according to our data. Variant chr5-71720635-CA-C is described in ClinVar as [Benign]. Clinvar id is 1290297.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CARTPT	NM_004291.4	c.*21delA		3_prime_UTR_variant	3/3	ENST00000296777.5	NP_004282.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CARTPT	ENST00000296777.5	c.*21delA		3_prime_UTR_variant	3/3	1	NM_004291.4	ENSP00000296777.4
CARTPT	ENST00000513096.1	n.514delA		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.0809 AC: 12308 AN: 152138 Hom.: 622 Cov.: 31

Gnomad AFR AF: 0.0187

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0907

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0889

Gnomad OTH AF: 0.0683

GnomAD3 exomes AF: 0.118 AC: 23942 AN: 203390 Hom.: 1608 AF XY: 0.117 AC XY: 12733 AN XY: 108404

Gnomad AFR exome AF: 0.0159

Gnomad AMR exome AF: 0.188

Gnomad ASJ exome AF: 0.0885

Gnomad EAS exome AF: 0.150

Gnomad SAS exome AF: 0.150

Gnomad FIN exome AF: 0.147

Gnomad NFE exome AF: 0.0925

Gnomad OTH exome AF: 0.0957

GnomAD4 exome AF: 0.0987 AC: 138281 AN: 1400712 Hom.: 7513 Cov.: 22 AF XY: 0.0994 AC XY: 69201 AN XY: 695966

Gnomad4 AFR exome AF: 0.0139

Gnomad4 AMR exome AF: 0.177

Gnomad4 ASJ exome AF: 0.0830

Gnomad4 EAS exome AF: 0.133

Gnomad4 SAS exome AF: 0.146

Gnomad4 FIN exome AF: 0.140

Gnomad4 NFE exome AF: 0.0922

Gnomad4 OTH exome AF: 0.0942

GnomAD4 genome AF: 0.0808 AC: 12302 AN: 152256 Hom.: 623 Cov.: 31 AF XY: 0.0845 AC XY: 6293 AN XY: 74434

Gnomad4 AFR AF: 0.0186

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.0907

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.0889

Gnomad4 OTH AF: 0.0666

Alfa AF: 0.0488 Hom.: 43

Bravo AF: 0.0769

Asia WGS AF: 0.157 AC: 544 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs5868607; hg19: chr5-71016462;