Genetic Variant NM_019858.2:c.1215+113A>C (chr12-6826466-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.157

Publications

11 publications found

Variant links:

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]

GPR162 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 link	c.1215+113A>C		intron_variant	Intron 4 of 4	ENST00000311268.8	NP_062832.1	Q16538-1A0A0I9QPQ8
GPR162	NM_014449.2 link	c.363+113A>C		intron_variant	Intron 4 of 4		NP_055264.1	Q16538-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR162	ENST00000311268.8 link	c.1215+113A>C		intron_variant	Intron 4 of 4	1	NM_019858.2	ENSP00000311528.3		Q16538-1

Frequencies

GnomAD3 genomes

AF:

0.208

AC:

31651

AN:

152000

Hom.:

3440

Cov.:

show subpopulations

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.:

AF XY:

0.202

AC XY:

103879

AN XY:

513088

show subpopulations

African (AFR)

AF:

0.175

AC:

4180

AN:

23934

American (AMR)

AF:

0.283

AC:

7204

AN:

25484

Ashkenazi Jewish (ASJ)

AF:

0.221

AC:

3928

AN:

17744

East Asian (EAS)

AF:

0.326

AC:

11921

AN:

36588

South Asian (SAS)

AF:

0.0971

AC:

6023

AN:

62052

European-Finnish (FIN)

AF:

0.260

AC:

9249

AN:

35584

Middle Eastern (MID)

AF:

0.171

AC:

768

AN:

4488

European-Non Finnish (NFE)

AF:

0.206

AC:

159387

AN:

774482

Other (OTH)

AF:

0.208

AC:

9381

AN:

45102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

8530

17060

25589

34119

42649

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5156

10312

15468

20624

25780

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.208

AC:

31677

AN:

152118

Hom.:

3443

Cov.:

AF XY:

0.211

AC XY:

15658

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.183

AC:

7575

AN:

41486

American (AMR)

AF:

0.233

AC:

3568

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.219

AC:

760

AN:

3468

East Asian (EAS)

AF:

0.354

AC:

1826

AN:

5162

South Asian (SAS)

AF:

0.102

AC:

491

AN:

4830

European-Finnish (FIN)

AF:

0.268

AC:

2837

AN:

10588

Middle Eastern (MID)

AF:

0.180

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.206

AC:

13999

AN:

67988

Other (OTH)

AF:

0.188

AC:

397

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1295

2590

3884

5179

6474

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

328

656

984

1312

1640

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.191

Hom.:

4671

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

(source)

DANN

Benign

0.75

PhyloP100

-0.16

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over