rs4963519

chr12-6822486-T-Cchr12-6822486-T-G

Variant summary

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

The NM_019858.2(GPR162):c.-432+586T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,062 control chromosomes in the GnomAD database, including 43,953 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 0.74 (43953 hom., cov: 31)
• Consequence: GPR162 NM_019858.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600

Genes affected

GPR162 (HGNC:16693): (G protein-coupled receptor 162) This gene was identified upon genomic analysis of a gene-dense region at human chromosome 12p13. It appears to be mainly expressed in the brain; however, its function is not known. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPR162	NM_019858.2	c.-432+586T>C		intron_variant		ENST00000311268.8
GPR162	NM_014449.2	c.-282+586T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPR162	ENST00000311268.8	c.-432+586T>C		intron_variant		1	NM_019858.2	P1

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112232 AN: 151946 Hom.: 43955 Cov.: 31

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.768

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.738 AC: 112251 AN: 152062 Hom.: 43953 Cov.: 31 AF XY: 0.735 AC XY: 54637 AN XY: 74316

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.819

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.791

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.762

Alfa AF: 0.796 Hom.: 10902

Bravo AF: 0.732

Asia WGS AF: 0.675 AC: 2346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.2
Dann	Benign	0.77

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: rs4963519; hg19: chr12-6931652;