rs2071081

Variant names:

• chr12-6826466-A-C
• rs2071081
• NM_019858.2:c.1215+113A>C

Your query was ambiguous. Multiple possible variants found:

• chr12-6826466-A-C
• chr12-6826466-A-G
• chr12-6826466-A-T

Variant summary

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

The NM_019858.2(GPR162):​c.1215+113A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 1,177,576 control chromosomes in the GnomAD database, including 26,447 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 0.21 (3443 hom., cov: 32)
  • Exomes 𝑓: 0.21 (23004 hom.)
• Consequence: GPR162 NM_019858.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR162	NM_019858.2	c.1215+113A>C		intron_variant	Intron 4 of 4	ENST00000311268.8	NP_062832.1
GPR162	NM_014449.2	c.363+113A>C		intron_variant	Intron 4 of 4		NP_055264.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR162	ENST00000311268.8	c.1215+113A>C		intron_variant	Intron 4 of 4	1	NM_019858.2	ENSP00000311528.3

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31651 AN: 152000 Hom.: 3440 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.187

GnomAD4 exome AF: 0.207 AC: 212041 AN: 1025458 Hom.: 23004 Cov.: 13 AF XY: 0.202 AC XY: 103879 AN XY: 513088

Gnomad4 AFR exome AF: 0.175

Gnomad4 AMR exome AF: 0.283

Gnomad4 ASJ exome AF: 0.221

Gnomad4 EAS exome AF: 0.326

Gnomad4 SAS exome AF: 0.0971

Gnomad4 FIN exome AF: 0.260

Gnomad4 NFE exome AF: 0.206

Gnomad4 OTH exome AF: 0.208

GnomAD4 genome AF: 0.208 AC: 31677 AN: 152118 Hom.: 3443 Cov.: 32 AF XY: 0.211 AC XY: 15658 AN XY: 74376

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.188

Alfa AF: 0.185 Hom.: 2946

Bravo AF: 0.208

Asia WGS AF: 0.185 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs2071081; hg19: chr12-6935631;