dbSNP rs11575893: CARTPT:c.159+172C>T (chr5-71719624-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

11 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt
CARTPT	NM_004291.4 link	c.159+172C>T		intron_variant	Intron 1 of 2	ENST00000296777.5	NP_004282.1	Q16568

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CARTPT	ENST00000296777.5 link	c.159+172C>T		intron_variant	Intron 1 of 2	1	NM_004291.4	ENSP00000296777.4		Q16568
CARTPT	ENST00000513096.1 link	n.46C>T		non_coding_transcript_exon_variant	Exon 1 of 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

African (AFR)

AF:

0.194

AC:

3551

AN:

18318

American (AMR)

AF:

0.184

AC:

5867

AN:

31880

Ashkenazi Jewish (ASJ)

AF:

0.0844

AC:

1526

AN:

18070

East Asian (EAS)

AF:

0.151

AC:

4914

AN:

32520

South Asian (SAS)

AF:

0.146

AC:

8508

AN:

58314

European-Finnish (FIN)

AF:

0.136

AC:

4489

AN:

32926

Middle Eastern (MID)

AF:

0.0773

AC:

269

AN:

3480

European-Non Finnish (NFE)

AF:

0.0892

AC:

40988

AN:

459362

Other (OTH)

AF:

0.108

AC:

3759

AN:

34690

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

3955

7910

11864

15819

19774

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

958

1916

2874

3832

4790

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.133

AC:

20207

AN:

152020

Hom.:

1512

Cov.:

AF XY:

0.134

AC XY:

9964

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.197

AC:

8148

AN:

41452

American (AMR)

AF:

0.142

AC:

2166

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0928

AC:

322

AN:

3468

East Asian (EAS)

AF:

0.171

AC:

881

AN:

5146

South Asian (SAS)

AF:

0.154

AC:

740

AN:

4812

European-Finnish (FIN)

AF:

0.147

AC:

1557

AN:

10604

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0896

AC:

6086

AN:

67938

Other (OTH)

AF:

0.106

AC:

224

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

879

1758

2636

3515

4394

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

216

432

648

864

1080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.105

Hom.:

2314

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

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Nov 10, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

2.0

(source)

DANN

Benign

0.92

PhyloP100

-0.43

PromoterAI

0.00060

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over