chr10-133127635-G-A

Variant names:

• chr10-133127635-G-A
• rs12257731
• NM_001083909.3:c.500+304G>A

Variant summary

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

The NM_001083909.3(ADGRA1):​c.500+304G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,086 control chromosomes in the GnomAD database, including 3,112 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 0.19 (3112 hom., cov: 33)
• Consequence: ADGRA1 NM_001083909.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 2 publications found

Genes affected

ADGRA1 (HGNC:13838): (adhesion G protein-coupled receptor A1) This gene encodes a protein that belongs to the adhesion family of G-protein-coupled receptors. Members of this family function in several sensory systems and regulate blood pressure, immune responses, food intake and development. A similar protein in rodents is thought to play a role in in the regulation of neuronal signaling pathways. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Mar 2014]

ENSG00000297384 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001083909.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRA1	NM_001083909.3	MANE Select	c.500+304G>A		intron	N/A	NP_001077378.1
	ADGRA1	NM_001291085.2		c.209+304G>A		intron	N/A	NP_001278014.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGRA1	ENST00000392607.8	TSL:5 MANE Select	c.500+304G>A		intron	N/A	ENSP00000376384.3
	ADGRA1	ENST00000392606.2	TSL:1	c.209+304G>A		intron	N/A	ENSP00000376383.2
	ENSG00000297384	ENST00000747638.1		n.-94C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28384 AN: 151968 Hom.: 3104 Cov.: 33

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.187 AC: 28410 AN: 152086 Hom.: 3112 Cov.: 33 AF XY: 0.194 AC XY: 14414 AN XY: 74322

African (AFR) AF: 0.228 AC: 9462 AN: 41476

American (AMR) AF: 0.270 AC: 4119 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 584 AN: 3468

East Asian (EAS) AF: 0.472 AC: 2436 AN: 5164

South Asian (SAS) AF: 0.249 AC: 1202 AN: 4822

European-Finnish (FIN) AF: 0.161 AC: 1711 AN: 10612

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8386 AN: 67948

Other (OTH) AF: 0.185 AC: 391 AN: 2108

Alfa AF: 0.176 Hom.: 1025

Bravo AF: 0.199

Asia WGS AF: 0.350 AC: 1213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.90
PhyloP100		-1.1
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: rs12257731; hg19: chr10-134941139;