Genetic Variant CARTPT:c.160-204A>T (chr5-71719676-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_004291.4(CARTPT):c.160-204A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CARTPT
NM_004291.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00700

Publications

19 publications found

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 Gene-Disease associations (from GenCC):

inherited obesity
Inheritance: AD, Unknown Classification: LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

CARTPT links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CARTPT	NM_004291.4 link	c.160-204A>T		intron_variant	Intron 1 of 2	ENST00000296777.5	NP_004282.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CARTPT	ENST00000296777.5 link	c.160-204A>T		intron_variant	Intron 1 of 2	1	NM_004291.4	ENSP00000296777.4
CARTPT	ENST00000513096.1 link	n.98A>T		non_coding_transcript_exon_variant	Exon 1 of 2	2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

591312

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

311996

African (AFR)

AF:

0.00

AC:

AN:

16224

American (AMR)

AF:

0.00

AC:

AN:

31326

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17404

East Asian (EAS)

AF:

0.00

AC:

AN:

32092

South Asian (SAS)

AF:

0.00

AC:

AN:

56282

European-Finnish (FIN)

AF:

0.00

AC:

AN:

32260

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2464

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

371850

Other (OTH)

AF:

0.00

AC:

AN:

31410

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

58013

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

5.1

(source)

DANN

Benign

0.76

PhyloP100

0.0070

PromoterAI

-0.012

Neutral

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over