9-127309965-C-T

Position:

• chr9-127309965-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032293.5(GARNL3):​c.220-1671C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,026 control chromosomes in the GnomAD database, including 7,878 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 0.29 (7878 hom., cov: 32)
• Consequence: GARNL3 NM_032293.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

Genes affected

GARNL3 (HGNC:25425): (GTPase activating Rap/RanGAP domain like 3) Predicted to enable GTPase activator activity. Predicted to be involved in activation of GTPase activity. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

GARNL3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GARNL3	NM_032293.5	c.220-1671C>T		intron_variant		ENST00000373387.9	NP_115669.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GARNL3	ENST00000373387.9	c.220-1671C>T		intron_variant		1	NM_032293.5	ENSP00000362485.4

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44093 AN: 151908 Hom.: 7873 Cov.: 32

Gnomad AFR AF: 0.0850

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.290 AC: 44099 AN: 152026 Hom.: 7878 Cov.: 32 AF XY: 0.297 AC XY: 22079 AN XY: 74336

Gnomad4 AFR AF: 0.0848

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.327

Alfa AF: 0.342 Hom.: 5862

Bravo AF: 0.286

Asia WGS AF: 0.204 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.96
DANN	Benign	0.50

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: rs7863451; hg19: chr9-130072244;