rs1669263

Positions:

• chr19-34325126-C-G
• chr19-34325126-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GARRE1	NM_014686.5	c.706-2295C>G		intron_variant		ENST00000299505.8	NP_055501.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GARRE1	ENST00000299505.8	c.706-2295C>G		intron_variant		1	NM_014686.5	ENSP00000299505	P1
GARRE1	ENST00000588338.6	n.264-23994C>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.785

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.777

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.70
DANN	Benign	0.35

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

Publications

LitVar

Other links and lift over

dbSNP: rs1669263; hg19: chr19-34816031;