chr11-67451438-A-G

Position:

• chr11-67451438-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_206997.1(GPR152):​c.1287T>C​(p.Ala429Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.026 in 1,613,952 control chromosomes in the GnomAD database, including 8,910 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 0.14 (4797 hom., cov: 33)
  • Exomes 𝑓: 0.014 (4113 hom.)
• Consequence: GPR152 NM_206997.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

Genes affected

GPR152 (HGNC:23622): (G protein-coupled receptor 152) Enables identical protein binding activity. Predicted to be involved in G protein-coupled receptor signaling pathway. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP7: Synonymous conserved (PhyloP=-0.411 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPR152	NM_206997.1	c.1287T>C	p.Ala429Ala	synonymous_variant	1/1	ENST00000312457.2	NP_996880.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPR152	ENST00000312457.2	c.1287T>C	p.Ala429Ala	synonymous_variant	1/1	6	NM_206997.1	ENSP00000310255.2

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20929 AN: 152062 Hom.: 4795 Cov.: 33

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0593

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00253

Gnomad OTH AF: 0.0981

GnomAD3 exomes AF: 0.0357 AC: 8936 AN: 250656 Hom.: 1897 AF XY: 0.0259 AC XY: 3513 AN XY: 135712

Gnomad AFR exome AF: 0.476

Gnomad AMR exome AF: 0.0247

Gnomad ASJ exome AF: 0.0000996

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.000719

Gnomad FIN exome AF: 0.0000465

Gnomad NFE exome AF: 0.00193

Gnomad OTH exome AF: 0.0196

GnomAD4 exome AF: 0.0143 AC: 20954 AN: 1461772 Hom.: 4113 Cov.: 32 AF XY: 0.0123 AC XY: 8959 AN XY: 727186

Gnomad4 AFR exome AF: 0.481

Gnomad4 AMR exome AF: 0.0281

Gnomad4 ASJ exome AF: 0.000115

Gnomad4 EAS exome AF: 0.0000504

Gnomad4 SAS exome AF: 0.000974

Gnomad4 FIN exome AF: 0.0000375

Gnomad4 NFE exome AF: 0.00142

Gnomad4 OTH exome AF: 0.0301

GnomAD4 genome AF: 0.138 AC: 20956 AN: 152180 Hom.: 4797 Cov.: 33 AF XY: 0.132 AC XY: 9812 AN XY: 74408

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.0591

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00253

Gnomad4 OTH AF: 0.0971

Alfa AF: 0.0581 Hom.: 1098

Bravo AF: 0.155

Asia WGS AF: 0.0210 AC: 75 AN: 3478

EpiCase AF: 0.00229

EpiControl AF: 0.00261

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.48

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: rs949252; hg19: chr11-67218909;