rs1306

Variant names:

• chr9-130137797-T-C
• rs1306
• NM_020960.5:c.*2676T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

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]

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR107	NM_020960.5	c.*2676T>C		3_prime_UTR_variant	Exon 18 of 18	ENST00000347136.11	NP_066011.2
GPR107	NM_001136557.2	c.*2676T>C		3_prime_UTR_variant	Exon 20 of 20		NP_001130029.1
GPR107	NM_001136558.2	c.*2676T>C		3_prime_UTR_variant	Exon 19 of 19		NP_001130030.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53544 AN: 152052 Hom.: 10326 Cov.: 33

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: 6 AN: 14 Hom.: 2 Cov.: 0 AF XY: 0.500 AC XY: 4 AN XY: 8

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.352 AC: 53564 AN: 152172 Hom.: 10323 Cov.: 33 AF XY: 0.352 AC XY: 26168 AN XY: 74404

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.372

Alfa AF: 0.415 Hom.: 17367

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
DANN	Benign	0.46
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs1306; hg19: chr9-132900076; COSMIC: COSV61278124; COSMIC: COSV61278124;