dbSNP rs2241228: GPRC5A:c.-8+389T>C (chr12-12892053-T-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_003979.4(GPRC5A):c.-8+389T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 151,168 control chromosomes in the GnomAD database, including 22,014 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 0.53 ( 21969 hom., cov: 29)

Exomes 𝑓: 0.58 ( 45 hom. )

Consequence

GPRC5A
NM_003979.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.58

Publications

0 publications found

Variant links:

Genes affected

GPRC5A (HGNC:9836): (G protein-coupled receptor class C group 5 member A) This gene encodes a member of the type 3 G protein-coupling receptor family, characterized by the signature 7-transmembrane domain motif. The encoded protein may be involved in interaction between retinoid acid and G protein signalling pathways. Retinoic acid plays a critical role in development, cellular growth, and differentiation. This gene may play a role in embryonic development and epithelial cell differentiation. [provided by RefSeq, Jul 2008]

GPRC5A 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=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPRC5A	NM_003979.4 link	c.-8+389T>C		intron_variant	Intron 1 of 3	ENST00000014914.6	NP_003970.1	Q8NFJ5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPRC5A	ENST00000014914.6 link	c.-8+389T>C		intron_variant	Intron 1 of 3	1	NM_003979.4	ENSP00000014914.6		Q8NFJ5

Frequencies

GnomAD3 genomes

AF:

0.534

AC:

80469

AN:

150792

Hom.:

21965

Cov.:

show subpopulations

Gnomad AFR

AF:

0.437

Gnomad AMI

AF:

0.655

Gnomad AMR

AF:

0.566

Gnomad ASJ

AF:

0.510

Gnomad EAS

AF:

0.435

Gnomad SAS

AF:

0.380

Gnomad FIN

AF:

0.624

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.590

Gnomad OTH

AF:

0.501

GnomAD4 exome

AF:

0.577

AC:

150

AN:

260

Hom.:

Cov.:

AF XY:

0.572

AC XY:

AN XY:

138

show subpopulations

African (AFR)

AF:

0.667

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.595

AC:

AN:

Middle Eastern (MID)

AF:

0.688

AC:

AN:

European-Non Finnish (NFE)

AF:

0.615

AC:

AN:

104

Other (OTH)

AF:

0.417

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.533

AC:

80500

AN:

150908

Hom.:

21969

Cov.:

AF XY:

0.531

AC XY:

39131

AN XY:

73730

show subpopulations

African (AFR)

AF:

0.437

AC:

17880

AN:

40960

American (AMR)

AF:

0.566

AC:

8576

AN:

15158

Ashkenazi Jewish (ASJ)

AF:

0.510

AC:

1763

AN:

3458

East Asian (EAS)

AF:

0.434

AC:

2207

AN:

5082

South Asian (SAS)

AF:

0.378

AC:

1794

AN:

4746

European-Finnish (FIN)

AF:

0.624

AC:

6513

AN:

10432

Middle Eastern (MID)

AF:

0.483

AC:

142

AN:

294

European-Non Finnish (NFE)

AF:

0.590

AC:

39984

AN:

67774

Other (OTH)

AF:

0.499

AC:

1044

AN:

2092

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

1885

3770

5656

7541

9426

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

698

1396

2094

2792

3490

<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:

0.554

Hom.:

13339

Bravo

AF:

0.528

Asia WGS

AF:

0.381

AC:

1330

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.8

(source)

DANN

Benign

0.70

PhyloP100

-1.6

PromoterAI

0.0084

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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