19-34325126-C-G

Variant names:

• chr19-34325126-C-G
• rs1669263
• NM_014686.5:c.706-2295C>G

Variant summary

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

The NM_014686.5(GARRE1):​c.706-2295C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 151,988 control chromosomes in the GnomAD database, including 46,230 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 0.78 (46230 hom., cov: 31)
• Consequence: GARRE1 NM_014686.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 2 publications found

Genes affected

GARRE1 (HGNC:29016): (granule associated Rac and RHOG effector 1) Enables CCR4-NOT complex binding activity and small GTPase binding activity. Involved in Rac protein signal transduction. Located in P-body. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014686.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GARRE1	NM_014686.5	MANE Select	c.706-2295C>G		intron	N/A	NP_055501.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GARRE1	ENST00000299505.8	TSL:1 MANE Select	c.706-2295C>G		intron	N/A	ENSP00000299505.4	O15063
	GARRE1	ENST00000899721.1		c.706-2295C>G		intron	N/A	ENSP00000569780.1
	GARRE1	ENST00000932925.1		c.706-2295C>G		intron	N/A	ENSP00000602984.1

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117684 AN: 151868 Hom.: 46179 Cov.: 31

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.775 AC: 117792 AN: 151988 Hom.: 46230 Cov.: 31 AF XY: 0.773 AC XY: 57419 AN XY: 74274

African (AFR) AF: 0.822 AC: 34066 AN: 41458

American (AMR) AF: 0.806 AC: 12310 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2717 AN: 3472

East Asian (EAS) AF: 0.381 AC: 1969 AN: 5170

South Asian (SAS) AF: 0.785 AC: 3779 AN: 4814

European-Finnish (FIN) AF: 0.750 AC: 7916 AN: 10548

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52449 AN: 67946

Other (OTH) AF: 0.777 AC: 1634 AN: 2104

Alfa AF: 0.763 Hom.: 5496

Bravo AF: 0.779

Asia WGS AF: 0.619 AC: 2155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.70
DANN	Benign	0.35
PhyloP100		-0.010
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: rs1669263; hg19: chr19-34816031;