dbSNP rs1306: 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
GPR107	NM_020960.5 link	c.*2676T>C	3_prime_UTR_variant	Exon 18 of 18	ENST00000347136.11	NP_066011.2	Q5VW38-2
GPR107	NM_001136557.2 link	c.*2676T>C	3_prime_UTR_variant	Exon 20 of 20		NP_001130029.1	Q5VW38-1
GPR107	NM_001136558.2 link	c.*2676T>C	3_prime_UTR_variant	Exon 19 of 19		NP_001130030.1	Q5VW38G5E994

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
GPR107	ENST00000347136.11 link	c.*2676T>C	3_prime_UTR_variant	Exon 18 of 18	1	NM_020960.5	ENSP00000336988.7	Q5VW38-2
GPR107	ENST00000372406.5 link	c.*2676T>C	3_prime_UTR_variant	Exon 20 of 20	1		ENSP00000361483.1	Q5VW38-1
GPR107	ENST00000372410.7 link	c.*2676T>C	3_prime_UTR_variant	Exon 19 of 19	5		ENSP00000361487.3	G5E994

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over