rs11575893

chr5-71719624-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_004291.4(CARTPT):c.159+172C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 841,580 control chromosomes in the GnomAD database, including 6,089 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.13 (1512 hom., cov: 32)
  • Exomes 𝑓: 0.11 (4577 hom.)
• Consequence: CARTPT NM_004291.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.428

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BP6: Variant 5-71719624-C-T is Benign according to our data. Variant chr5-71719624-C-T is described in ClinVar as [Benign]. Clinvar id is 1250951.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CARTPT	NM_004291.4	c.159+172C>T		intron_variant		ENST00000296777.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CARTPT	ENST00000296777.5	c.159+172C>T		intron_variant		1	NM_004291.4	P1
CARTPT	ENST00000513096.1	n.46C>T		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20177 AN: 151900 Hom.: 1504 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.0573

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.108

GnomAD4 exome AF: 0.107 AC: 73871 AN: 689560 Hom.: 4577 Cov.: 9 AF XY: 0.107 AC XY: 38525 AN XY: 358694

Gnomad4 AFR exome AF: 0.194

Gnomad4 AMR exome AF: 0.184

Gnomad4 ASJ exome AF: 0.0844

Gnomad4 EAS exome AF: 0.151

Gnomad4 SAS exome AF: 0.146

Gnomad4 FIN exome AF: 0.136

Gnomad4 NFE exome AF: 0.0892

Gnomad4 OTH exome AF: 0.108

GnomAD4 genome AF: 0.133 AC: 20207 AN: 152020 Hom.: 1512 Cov.: 32 AF XY: 0.134 AC XY: 9964 AN XY: 74316

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0928

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.0896

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0964 Hom.: 682

Bravo AF: 0.136

Asia WGS AF: 0.166 AC: 575 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

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	2.0
Dann	Benign	0.92

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: rs11575893; hg19: chr5-71015451; COSMIC: COSV57115469;