NM_019858.2:c.1215+113A>T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_019858.2(GPR162):​c.1215+113A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000469 in 1,179,090 control chromosomes in the GnomAD database, including 1 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 0.00018 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00051 (1 hom.)
• Consequence: GPR162 NM_019858.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 11 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR162	NM_019858.2	c.1215+113A>T		intron_variant	Intron 4 of 4	ENST00000311268.8	NP_062832.1
GPR162	NM_014449.2	c.363+113A>T		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>T		intron_variant	Intron 4 of 4	1	NM_019858.2	ENSP00000311528.3

Frequencies

GnomAD3 genomes AF: 0.000178 AC: 27 AN: 152048 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000368

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000512 AC: 526 AN: 1027042 Hom.: 1 Cov.: 13 AF XY: 0.000524 AC XY: 269 AN XY: 513834

African (AFR) AF: 0.0000835 AC: 2 AN: 23966

American (AMR) AF: 0.00 AC: 0 AN: 25538

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17762

East Asian (EAS) AF: 0.0000546 AC: 2 AN: 36624

South Asian (SAS) AF: 0.00 AC: 0 AN: 62080

European-Finnish (FIN) AF: 0.0000842 AC: 3 AN: 35610

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4488

European-Non Finnish (NFE) AF: 0.000637 AC: 494 AN: 775812

Other (OTH) AF: 0.000554 AC: 25 AN: 45162

GnomAD4 genome AF: 0.000178 AC: 27 AN: 152048 Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10 AN XY: 74266

African (AFR) AF: 0.0000483 AC: 2 AN: 41388

American (AMR) AF: 0.00 AC: 0 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.00 AC: 0 AN: 4834

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10588

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.000368 AC: 25 AN: 68010

Other (OTH) AF: 0.00 AC: 0 AN: 2090

Alfa AF: 0.00 Hom.: 4671

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.82
PhyloP100		-0.16

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2071081; hg19: chr12-6935631;