Genetic Variant GPR107:c.*2676T>C (chr9-130137797-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020960.5(GPR107):c.*2676T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,186 control chromosomes in the GnomAD database, including 10,325 homozygotes. 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: 𝑓 0.35 ( 10323 hom., cov: 33)

Exomes 𝑓: 0.43 ( 2 hom. )

Consequence

GPR107
NM_020960.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01

Publications

18 publications found

Variant links:

Genes affected

GPR107 (HGNC:17830): (G protein-coupled receptor 107) Predicted to enable clathrin heavy chain binding activity. Predicted to be involved in clathrin-dependent endocytosis. Located in Golgi apparatus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

GPR107 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020960.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
GPR107	NM_020960.5	MANE Select	c.*2676T>C	3_prime_UTR	Exon 18 of 18	NP_066011.2
GPR107	NM_001136557.2		c.*2676T>C	3_prime_UTR	Exon 20 of 20	NP_001130029.1
GPR107	NM_001136558.2		c.*2676T>C	3_prime_UTR	Exon 19 of 19	NP_001130030.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
GPR107	ENST00000347136.11	TSL:1 MANE Select	c.*2676T>C	3_prime_UTR	Exon 18 of 18	ENSP00000336988.7
GPR107	ENST00000372406.5	TSL:1	c.*2676T>C	3_prime_UTR	Exon 20 of 20	ENSP00000361483.1
GPR107	ENST00000372410.7	TSL:5	c.*2676T>C	3_prime_UTR	Exon 19 of 19	ENSP00000361487.3

Frequencies

GnomAD3 genomes

AF:

0.352

AC:

53544

AN:

152052

Hom.:

10326

Cov.:

show subpopulations

Gnomad AFR

AF:

0.210

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.419

Gnomad ASJ

AF:

0.447

Gnomad EAS

AF:

0.160

Gnomad SAS

AF:

0.262

Gnomad FIN

AF:

0.422

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.429

Gnomad OTH

AF:

0.372

GnomAD4 exome

AF:

0.429

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.750

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.352

AC:

53564

AN:

152172

Hom.:

10323

Cov.:

AF XY:

0.352

AC XY:

26168

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.210

AC:

8698

AN:

41512

American (AMR)

AF:

0.419

AC:

6403

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.447

AC:

1549

AN:

3468

East Asian (EAS)

AF:

0.160

AC:

828

AN:

5174

South Asian (SAS)

AF:

0.264

AC:

1272

AN:

4822

European-Finnish (FIN)

AF:

0.422

AC:

4468

AN:

10580

Middle Eastern (MID)

AF:

0.384

AC:

113

AN:

294

European-Non Finnish (NFE)

AF:

0.429

AC:

29160

AN:

68014

Other (OTH)

AF:

0.372

AC:

786

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1765

3530

5294

7059

8824

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

524

1048

1572

2096

2620

<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:

0.406

Hom.:

26084

Bravo

AF:

0.346

Asia WGS

AF:

0.212

AC:

740

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.074

(source)

DANN

Benign

0.46

PhyloP100

-1.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over