Genetic Variant GPR155:p.Ser631Asn (chr2-174446732-C-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_152529.7(GPR155):c.1892G>A(p.Ser631Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,606 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S631T) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

GPR155
NM_152529.7 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.583

Publications

0 publications found

Variant links:

Genes affected

GPR155 (HGNC:22951): (G protein-coupled receptor 155) Involved in cognition. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

GPR155 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.16972241).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152529.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
GPR155	NM_152529.7	MANE Select	c.1892G>A	p.Ser631Asn	missense	Exon 12 of 16	NP_689742.4
GPR155	NM_001033045.4		c.1892G>A	p.Ser631Asn	missense	Exon 13 of 17	NP_001028217.1	Q7Z3F1
GPR155	NM_001267050.2		c.1892G>A	p.Ser631Asn	missense	Exon 13 of 17	NP_001253979.1	Q7Z3F1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
GPR155	ENST00000392552.7	TSL:1 MANE Select	c.1892G>A	p.Ser631Asn	missense	Exon 12 of 16	ENSP00000376335.2	Q7Z3F1
GPR155	ENST00000295500.8	TSL:1	c.1892G>A	p.Ser631Asn	missense	Exon 13 of 17	ENSP00000295500.4	Q7Z3F1
GPR155	ENST00000392551.6	TSL:1	c.1892G>A	p.Ser631Asn	missense	Exon 13 of 17	ENSP00000376334.2	Q7Z3F1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

6.84e-7

AC:

AN:

1461606

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

727126

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33470

American (AMR)

AF:

0.00

AC:

AN:

44670

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26130

East Asian (EAS)

AF:

0.00

AC:

AN:

39692

South Asian (SAS)

AF:

0.00

AC:

AN:

86238

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53404

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

8.99e-7

AC:

AN:

1111846

Other (OTH)

AF:

0.00

AC:

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.090

BayesDel_addAF

Benign

-0.32

BayesDel_noAF

Benign

-0.70

CADD

Benign

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.023

Eigen

Benign

-0.029

Eigen_PC

Benign

0.14

FATHMM_MKL

Benign

0.69

LIST_S2

Benign

0.72

M_CAP

Benign

0.0080

MetaRNN

Benign

0.17

MetaSVM

Benign

-0.89

MutationAssessor

Benign

1.5

PhyloP100

0.58

PrimateAI

Uncertain

0.50

PROVEAN

Benign

-0.64

REVEL

Benign

0.074

Sift

Benign

0.14

Sift4G

Benign

0.18

Polyphen

0.0030

Vest4

0.24

MutPred

0.22

Loss of catalytic residue at S631 (P = 0.0326)

MVP

0.40

MPC

0.15

ClinPred

0.33

GERP RS

5.5

Varity_R

0.087

gMVP

0.20

Mutation Taster

=93/7

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over