Variant 5-71719624-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.428

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 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_multiple_submitters_no_conflicts, 2 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	Protein	UniProt
CARTPT	NM_004291.4 linkuse as main transcript	c.159+172C>T		intron_variant		ENST00000296777.5	NP_004282.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CARTPT	ENST00000296777.5 linkuse as main transcript	c.159+172C>T		intron_variant		1	NM_004291.4	ENSP00000296777	P1
CARTPT	ENST00000513096.1 linkuse as main transcript	n.46C>T		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes

AF:

0.133

AC:

20177

AN:

151900

Hom.:

1504

Cov.:

show subpopulations

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.:

AF XY:

0.107

AC XY:

38525

AN XY:

358694

show subpopulations

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.:

AF XY:

0.134

AC XY:

9964

AN XY:

74316

show subpopulations

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:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over