rs1569019

Variant names:

• chr12-131091646-C-A
• rs1569019
• NM_198827.5:c.1671+6983C>A

Your query was ambiguous. Multiple possible variants found:

• chr12-131091646-C-A
• chr12-131091646-C-G
• chr12-131091646-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198827.5(ADGRD1):​c.1671+6983C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0815 in 152,242 control chromosomes in the GnomAD database, including 659 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 0.081 (659 hom., cov: 33)
• Consequence: ADGRD1 NM_198827.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 16 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.22).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198827.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRD1	NM_198827.5	MANE Select	c.1671+6983C>A		intron	N/A	NP_942122.2
	ADGRD1	NM_001330497.2		c.1767+6983C>A		intron	N/A	NP_001317426.1	Q6QNK2-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRD1	ENST00000261654.10	TSL:1 MANE Select	c.1671+6983C>A		intron	N/A	ENSP00000261654.5	Q6QNK2-1
	ADGRD1	ENST00000535015.5	TSL:1	c.1767+6983C>A		intron	N/A	ENSP00000444425.1	Q6QNK2-4
	ADGRD1	ENST00000543617.2	TSL:1	c.228+6983C>A		intron	N/A	ENSP00000438021.1	Q6QNK2-3

Frequencies

GnomAD3 genomes AF: 0.0815 AC: 12403 AN: 152122 Hom.: 658 Cov.: 33

Gnomad AFR AF: 0.0217

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.0687

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.0160

Gnomad SAS AF: 0.0814

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.0880

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0815 AC: 12407 AN: 152242 Hom.: 659 Cov.: 33 AF XY: 0.0822 AC XY: 6116 AN XY: 74428

African (AFR) AF: 0.0219 AC: 911 AN: 41552

American (AMR) AF: 0.0686 AC: 1049 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0974 AC: 338 AN: 3470

East Asian (EAS) AF: 0.0154 AC: 80 AN: 5188

South Asian (SAS) AF: 0.0815 AC: 393 AN: 4822

European-Finnish (FIN) AF: 0.115 AC: 1222 AN: 10598

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8060 AN: 68012

Other (OTH) AF: 0.0871 AC: 184 AN: 2112

Alfa AF: 0.104 Hom.: 3329

Bravo AF: 0.0738

Asia WGS AF: 0.0390 AC: 135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	2.3
DANN	Benign	0.68
PhyloP100		-0.018
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1569019; hg19: chr12-131576191;