Variant 16-67483276-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001138.2(AGRP):c.123G>A(p.Glu41=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0548 in 1,585,708 control chromosomes in the GnomAD database, including 4,162 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.10 ( 1366 hom., cov: 33)

Exomes 𝑓: 0.050 ( 2796 hom. )

Consequence

AGRP
NM_001138.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.464

Variant links:

Genes affected

AGRP (HGNC:330): (agouti related neuropeptide) This gene encodes an antagonist of the melanocortin-3 and melanocortin-4 receptor. It appears to regulate hypothalamic control of feeding behavior via melanocortin receptor and/or intracellular calcium regulation, and thus plays a role in weight homeostasis. Mutations in this gene have been associated with late on-set obesity. [provided by RefSeq, Dec 2009]

AGRP links:

ATP6V0D1-DT (HGNC:55268): (ATP6V0D1 divergent transcript)

ATP6V0D1-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BP6

Variant 16-67483276-C-T is Benign according to our data. Variant chr16-67483276-C-T is described in ClinVar as [Benign]. Clinvar id is 1280192.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.464 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGRP	NM_001138.2 linkuse as main transcript	c.123G>A	p.Glu41=	synonymous_variant	2/4	ENST00000290953.3
ATP6V0D1-DT	NR_184227.1 linkuse as main transcript	n.127-834C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGRP	ENST00000290953.3 linkuse as main transcript	c.123G>A	p.Glu41=	synonymous_variant	2/4	1	NM_001138.2	P1
ATP6V0D1-DT	ENST00000656196.1 linkuse as main transcript	n.207-834C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.100

AC:

15228

AN:

152122

Hom.:

1356

Cov.:

show subpopulations

Gnomad AFR

AF:

0.243

Gnomad AMI

AF:

0.0592

Gnomad AMR

AF:

0.0641

Gnomad ASJ

AF:

0.0579

Gnomad EAS

AF:

0.00385

Gnomad SAS

AF:

0.0726

Gnomad FIN

AF:

0.0374

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.0426

Gnomad OTH

AF:

0.0957

GnomAD3 exomes

AF:

0.0582

AC:

12582

AN:

216048

Hom.:

665

AF XY:

0.0568

AC XY:

6664

AN XY:

117230

show subpopulations

Gnomad AFR exome

AF:

0.246

Gnomad AMR exome

AF:

0.0389

Gnomad ASJ exome

AF:

0.0611

Gnomad EAS exome

AF:

0.00256

Gnomad SAS exome

AF:

0.0804

Gnomad FIN exome

AF:

0.0378

Gnomad NFE exome

AF:

0.0441

Gnomad OTH exome

AF:

0.0549

GnomAD4 exome

AF:

0.0499

AC:

71557

AN:

1433470

Hom.:

2796

Cov.:

AF XY:

0.0500

AC XY:

35531

AN XY:

710872

show subpopulations

Gnomad4 AFR exome

AF:

0.256

Gnomad4 AMR exome

AF:

0.0412

Gnomad4 ASJ exome

AF:

0.0625

Gnomad4 EAS exome

AF:

0.00168

Gnomad4 SAS exome

AF:

0.0768

Gnomad4 FIN exome

AF:

0.0414

Gnomad4 NFE exome

AF:

0.0429

Gnomad4 OTH exome

AF:

0.0639

GnomAD4 genome

AF:

0.100

AC:

15278

AN:

152238

Hom.:

1366

Cov.:

AF XY:

0.0980

AC XY:

7297

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.244

Gnomad4 AMR

AF:

0.0640

Gnomad4 ASJ

AF:

0.0579

Gnomad4 EAS

AF:

0.00386

Gnomad4 SAS

AF:

0.0722

Gnomad4 FIN

AF:

0.0374

Gnomad4 NFE

AF:

0.0427

Gnomad4 OTH

AF:

0.0952

Alfa

AF:

0.0595

Hom.:

262

Bravo

AF:

0.106

Asia WGS

AF:

0.0600

AC:

208

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 09, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

5.3

DANN

Benign

0.70

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