3-120165816-G-T

Variant names:

• chr3-120165816-G-T
• rs1488763
• NM_153002.3:c.*1216C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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]

GSK3B-DT (HGNC:55635): (GSK3B divergent transcript)

LOC105374065 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GPR156	NM_153002.3	c.*1216C>A		3_prime_UTR_variant	Exon 10 of 10	ENST00000464295.6	NP_694547.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR156	ENST00000464295.6	c.*1216C>A		3_prime_UTR_variant	Exon 10 of 10	5	NM_153002.3	ENSP00000417261.1
GPR156	ENST00000495912.5	n.*2724C>A		non_coding_transcript_exon_variant	Exon 4 of 4	5		ENSP00000417191.1
GPR156	ENST00000495912.5	n.*2724C>A		3_prime_UTR_variant	Exon 4 of 4	5		ENSP00000417191.1
GSK3B-DT	ENST00000834988.1	n.310-17694G>T		intron_variant	Intron 2 of 3

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

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: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.692 AC: 18 AN: 26

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.432 AC: 17886 AN: 41440

American (AMR) AF: 0.587 AC: 8984 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2340 AN: 3470

East Asian (EAS) AF: 0.208 AC: 1074 AN: 5162

South Asian (SAS) AF: 0.481 AC: 2317 AN: 4818

European-Finnish (FIN) AF: 0.675 AC: 7147 AN: 10582

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47340 AN: 67980

Other (OTH) AF: 0.603 AC: 1275 AN: 2114

Alfa AF: 0.647 Hom.: 52730

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
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1488763; hg19: chr3-119884663;