Variant 17-81810847-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_000160.5(GCGR):c.186C>T(p.Phe62Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000402 in 1,536,722 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00094 ( 0 hom., cov: 33)

Exomes 𝑓: 0.00034 ( 3 hom. )

Consequence

GCGR
NM_000160.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.23

Variant links:

Genes affected

GCGR (HGNC:4192): (glucagon receptor) The protein encoded by this gene is a glucagon receptor that is important in controlling blood glucose levels. Defects in this gene are a cause of non-insulin-dependent diabetes mellitus (NIDDM).[provided by RefSeq, Jan 2010]

GCGR links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BP6

Variant 17-81810847-C-T is Benign according to our data. Variant chr17-81810847-C-T is described in ClinVar as [Benign]. Clinvar id is 2145129.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.23 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GCGR	NM_000160.5 link	c.186C>T	p.Phe62Phe	synonymous_variant	4/14	ENST00000400723.8	NP_000151.1	P47871
GCGR	XM_011523539.2 link	c.110C>T	p.Ser37Leu	missense_variant	2/12		XP_011521841.1
GCGR	XM_006722277.2 link	c.186C>T	p.Phe62Phe	synonymous_variant	4/14		XP_006722340.1	P47871
GCGR	XM_017024446.2 link	c.180C>T	p.Phe60Phe	synonymous_variant	4/14		XP_016879935.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
GCGR	ENST00000400723.8 link	c.186C>T	p.Phe62Phe	synonymous_variant	4/14	1	NM_000160.5	ENSP00000383558.3	P47871
GCGR	ENST00000570996.5 link	c.186C>T	p.Phe62Phe	synonymous_variant	4/12	2		ENSP00000460976.1	I3L454
GCGR	ENST00000573428.1 link	c.186C>T	p.Phe62Phe	synonymous_variant	4/4	4		ENSP00000458930.1	I3L1L8
GCGR	ENST00000574283.2 link	n.270C>T		non_coding_transcript_exon_variant	2/3	5

Frequencies

GnomAD3 genomes

AF:

0.000940

AC:

143

AN:

152128

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0111

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000338

Gnomad OTH

AF:

0.000956

GnomAD3 exomes

AF:

0.000437

AC:

AN:

141944

Hom.:

AF XY:

0.000329

AC XY:

AN XY:

75930

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000407

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00922

Gnomad NFE exome

AF:

0.000154

Gnomad OTH exome

AF:

0.000473

GnomAD4 exome

AF:

0.000342

AC:

474

AN:

1384476

Hom.:

Cov.:

AF XY:

0.000304

AC XY:

208

AN XY:

683184

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0112

Gnomad4 NFE exome

AF:

0.0000640

Gnomad4 OTH exome

AF:

0.000345

GnomAD4 genome

AF:

0.000939

AC:

143

AN:

152246

Hom.:

Cov.:

AF XY:

0.00130

AC XY:

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0111

Gnomad4 NFE

AF:

0.000338

Gnomad4 OTH

AF:

0.000946

Alfa

AF:

0.000789

Hom.:

Bravo

AF:

0.0000831

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

Labcorp Genetics (formerly Invitae), Labcorp

Dec 25, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

3.7

DANN

Benign

0.61

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