Genetic Variant ADGRD1:c.2436+203A>G (chr12-131137217-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_198827.5(ADGRD1):c.2436+203A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 610,648 control chromosomes in the GnomAD database, including 124,772 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 0.64 ( 31127 hom., cov: 34)

Exomes 𝑓: 0.63 ( 93645 hom. )

Consequence

ADGRD1
NM_198827.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.29

Variant links:

Genes affected

ADGRD1 (HGNC:19893): (adhesion G protein-coupled receptor D1) The adhesion G-protein-coupled receptors (GPCRs), including GPR133, are membrane-bound proteins with long N termini containing multiple domains. GPCRs, or GPRs, contain 7 transmembrane domains and transduce extracellular signals through heterotrimeric G proteins (summary by Bjarnadottir et al., 2004 [PubMed 15203201]).[supplied by OMIM, Nov 2010]

ADGRD1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.25).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRD1	NM_198827.5 link	c.2436+203A>G		intron_variant	Intron 23 of 24	ENST00000261654.10	NP_942122.2	Q6QNK2-1Q9NSM3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRD1	ENST00000261654.10 link	c.2436+203A>G		intron_variant	Intron 23 of 24	1	NM_198827.5	ENSP00000261654.5		Q6QNK2-1

Frequencies

GnomAD3 genomes

AF:

0.636

AC:

96589

AN:

151962

Hom.:

31080

Cov.:

show subpopulations

Gnomad AFR

AF:

0.663

Gnomad AMI

AF:

0.497

Gnomad AMR

AF:

0.512

Gnomad ASJ

AF:

0.695

Gnomad EAS

AF:

0.440

Gnomad SAS

AF:

0.631

Gnomad FIN

AF:

0.568

Gnomad MID

AF:

0.744

Gnomad NFE

AF:

0.671

Gnomad OTH

AF:

0.644

GnomAD4 exome

AF:

0.635

AC:

291070

AN:

458570

Hom.:

93645

AF XY:

0.638

AC XY:

155532

AN XY:

243960

show subpopulations

Gnomad4 AFR exome

AF:

0.662

Gnomad4 AMR exome

AF:

0.434

Gnomad4 ASJ exome

AF:

0.698

Gnomad4 EAS exome

AF:

0.441

Gnomad4 SAS exome

AF:

0.632

Gnomad4 FIN exome

AF:

0.603

Gnomad4 NFE exome

AF:

0.669

Gnomad4 OTH exome

AF:

0.648

GnomAD4 genome

AF:

0.636

AC:

96689

AN:

152078

Hom.:

31127

Cov.:

AF XY:

0.627

AC XY:

46621

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.663

Gnomad4 AMR

AF:

0.512

Gnomad4 ASJ

AF:

0.695

Gnomad4 EAS

AF:

0.440

Gnomad4 SAS

AF:

0.632

Gnomad4 FIN

AF:

0.568

Gnomad4 NFE

AF:

0.671

Gnomad4 OTH

AF:

0.646

Alfa

AF:

0.654

Hom.:

34214

Bravo

AF:

0.625

Asia WGS

AF:

0.556

AC:

1933

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.3

CADD

Benign

0.43

DANN

Benign

0.45

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over