rs9289143

Variant names:

• chr3-120199814-C-A
• rs9289143
• NM_153002.3:c.234-6390G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-120199814-C-A
• chr3-120199814-C-G

Variant summary

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

The NM_153002.3(GPR156):​c.234-6390G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.901 in 152,208 control chromosomes in the GnomAD database, including 61,908 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 0.90 (61908 hom., cov: 31)
• Consequence: GPR156 NM_153002.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 4 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]

GPR156 Gene-Disease associations (from GenCC):

• hearing loss, autosomal recessive 121

  Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153002.3. 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
	GPR156	NM_153002.3	MANE Select	c.234-6390G>T		intron	N/A	NP_694547.2
	GPR156	NM_001168271.2		c.234-6390G>T		intron	N/A	NP_001161743.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR156	ENST00000464295.6	TSL:5 MANE Select	c.234-6390G>T		intron	N/A	ENSP00000417261.1
	GPR156	ENST00000461057.1	TSL:1	c.234-6390G>T		intron	N/A	ENSP00000418758.1
	GPR156	ENST00000495912.5	TSL:5	n.234-26344G>T		intron	N/A	ENSP00000417191.1

Frequencies

GnomAD3 genomes AF: 0.901 AC: 137080 AN: 152090 Hom.: 61854 Cov.: 31

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.915

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.901 AC: 137196 AN: 152208 Hom.: 61908 Cov.: 31 AF XY: 0.901 AC XY: 67014 AN XY: 74412

African (AFR) AF: 0.862 AC: 35766 AN: 41504

American (AMR) AF: 0.924 AC: 14136 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.932 AC: 3236 AN: 3472

East Asian (EAS) AF: 0.921 AC: 4759 AN: 5170

South Asian (SAS) AF: 0.854 AC: 4117 AN: 4820

European-Finnish (FIN) AF: 0.937 AC: 9935 AN: 10604

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.915 AC: 62244 AN: 68024

Other (OTH) AF: 0.909 AC: 1921 AN: 2114

Alfa AF: 0.906 Hom.: 33796

Bravo AF: 0.902

Asia WGS AF: 0.896 AC: 3115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	2.1
DANN	Benign	0.86
PhyloP100		-0.075
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: rs9289143; hg19: chr3-119918661;