NM_198827.5:c.1671+7237C>T

Variant names:

• chr12-131091900-C-T
• rs1976930
• NM_198827.5:c.1671+7237C>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+7237C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0897 in 152,320 control chromosomes in the GnomAD database, including 707 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 0.090 (704 hom., cov: 33)
  • Exomes 𝑓: 0.14 (3 hom.)
• Consequence: ADGRD1 NM_198827.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.821
• Publications: 4 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=-1.21).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRD1	NM_198827.5	c.1671+7237C>T		intron_variant	Intron 15 of 24	ENST00000261654.10	NP_942122.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRD1	ENST00000261654.10	c.1671+7237C>T		intron_variant	Intron 15 of 24	1	NM_198827.5	ENSP00000261654.5

Frequencies

GnomAD3 genomes AF: 0.0897 AC: 13641 AN: 152104 Hom.: 702 Cov.: 33

Gnomad AFR AF: 0.0495

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0749

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.0160

Gnomad SAS AF: 0.0818

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.0947

GnomAD4 exome AF: 0.143 AC: 14 AN: 98 Hom.: 3 Cov.: 0 AF XY: 0.114 AC XY: 8 AN XY: 70

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 3 AN: 12

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.134 AC: 11 AN: 82

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0897 AC: 13653 AN: 152222 Hom.: 704 Cov.: 33 AF XY: 0.0903 AC XY: 6721 AN XY: 74432

African (AFR) AF: 0.0498 AC: 2069 AN: 41524

American (AMR) AF: 0.0747 AC: 1142 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0974 AC: 338 AN: 3472

East Asian (EAS) AF: 0.0154 AC: 80 AN: 5186

South Asian (SAS) AF: 0.0819 AC: 395 AN: 4822

European-Finnish (FIN) AF: 0.115 AC: 1219 AN: 10606

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8043 AN: 67998

Other (OTH) AF: 0.0938 AC: 198 AN: 2112

Alfa AF: 0.105 Hom.: 182

Bravo AF: 0.0827

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	5.8
DANN	Benign	0.53
PhyloP100		0.82
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: rs1976930; hg19: chr12-131576445;