rs10845606

Variant names:

• chr12-12681960-C-A
• rs10845606
• NM_006143.3:c.-23+2391G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-12681960-C-A
• chr12-12681960-C-G
• chr12-12681960-C-T

Variant summary

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

The NM_006143.3(GPR19):​c.-23+2391G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,140 control chromosomes in the GnomAD database, including 2,348 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 0.16 (2348 hom., cov: 32)
• Consequence: GPR19 NM_006143.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 19 publications found

Genes affected

GPR19 (HGNC:4473): (G protein-coupled receptor 19) Predicted to enable G protein-coupled receptor activity. Predicted to be involved in G protein-coupled receptor signaling pathway. Located in cilium. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000257004 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006143.3. 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
	GPR19	NM_006143.3	MANE Select	c.-23+2391G>T		intron	N/A	NP_006134.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR19	ENST00000651487.1	MANE Select	c.-23+2391G>T		intron	N/A	ENSP00000498976.1
	GPR19	ENST00000332427.6	TSL:4	c.-23+2391G>T		intron	N/A	ENSP00000333744.2
	GPR19	ENST00000540510.1	TSL:2	c.-23+2391G>T		intron	N/A	ENSP00000441832.1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23769 AN: 152022 Hom.: 2351 Cov.: 32

Gnomad AFR AF: 0.0427

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.156 AC: 23753 AN: 152140 Hom.: 2348 Cov.: 32 AF XY: 0.152 AC XY: 11309 AN XY: 74378

African (AFR) AF: 0.0425 AC: 1765 AN: 41526

American (AMR) AF: 0.153 AC: 2341 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 564 AN: 3470

East Asian (EAS) AF: 0.300 AC: 1549 AN: 5168

South Asian (SAS) AF: 0.181 AC: 871 AN: 4818

European-Finnish (FIN) AF: 0.130 AC: 1381 AN: 10592

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14730 AN: 67982

Other (OTH) AF: 0.179 AC: 378 AN: 2110

Alfa AF: 0.192 Hom.: 5931

Bravo AF: 0.153

Asia WGS AF: 0.243 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.5
DANN	Benign	0.71
PhyloP100		-0.36
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: rs10845606; hg19: chr12-12834894;