3-120165816-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153002.3(GPR156):c.*1216C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 152,090 control chromosomes in the GnomAD database, including 27,610 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 0.59 (27604 hom., cov: 31)
  • Exomes 𝑓: 0.68 (6 hom.)
• Consequence: GPR156 NM_153002.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

GPR156 (HGNC:20844): (G protein-coupled receptor 156) G protein-coupled receptors (GPCRs) are a large superfamily of cell surface receptors characterized by 7 helical transmembrane domains, together with N-terminal extracellular and C-terminal intracellular domains.[supplied by OMIM, Mar 2008]

LOC105374065 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPR156	NM_153002.3	c.*1216C>A		3_prime_UTR_variant	10/10	ENST00000464295.6
LOC105374065	XR_924392.3	n.284-17694G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPR156	ENST00000464295.6	c.*1216C>A		3_prime_UTR_variant	10/10	5	NM_153002.3	A2
GPR156	ENST00000495912.5	c.*2724C>A		3_prime_UTR_variant, NMD_transcript_variant	4/4	5

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89199 AN: 151944 Hom.: 27604 Cov.: 31

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.608

GnomAD4 exome AF: 0.679 AC: 19 AN: 28 Hom.: 6 Cov.: 0 AF XY: 0.692 AC XY: 18 AN XY: 26

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.692

GnomAD4 genome AF: 0.587 AC: 89222 AN: 152062 Hom.: 27604 Cov.: 31 AF XY: 0.582 AC XY: 43302 AN XY: 74360

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.603

Alfa AF: 0.678 Hom.: 38977

Bravo AF: 0.573

Asia WGS AF: 0.363 AC: 1266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.13
Dann	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1488763; hg19: chr3-119884663;