9-127309965-C-T

Variant names:

• chr9-127309965-C-T
• rs7863451
• NM_032293.5:c.220-1671C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032293.5. 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
	GARNL3	NM_032293.5	MANE Select	c.220-1671C>T		intron	N/A	NP_115669.3
	GARNL3	NM_001286779.2		c.154-1671C>T		intron	N/A	NP_001273708.1	Q5VVW2-5
	GARNL3	NR_104591.2		n.324-1671C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GARNL3	ENST00000373387.9	TSL:1 MANE Select	c.220-1671C>T		intron	N/A	ENSP00000362485.4	Q5VVW2-1
	GARNL3	ENST00000435213.6	TSL:2	c.154-1671C>T		intron	N/A	ENSP00000396205.2	Q5VVW2-5
	GARNL3	ENST00000439286.5	TSL:5	c.289-1671C>T		intron	N/A	ENSP00000400579.1	Q5JS19

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

African (AFR) AF: 0.0848 AC: 3518 AN: 41492

American (AMR) AF: 0.442 AC: 6747 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1034 AN: 3468

East Asian (EAS) AF: 0.212 AC: 1097 AN: 5186

South Asian (SAS) AF: 0.263 AC: 1264 AN: 4802

European-Finnish (FIN) AF: 0.453 AC: 4772 AN: 10538

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24364 AN: 67960

Other (OTH) AF: 0.327 AC: 690 AN: 2108

Alfa AF: 0.347 Hom.: 7719

Bravo AF: 0.286

Asia WGS AF: 0.204 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.96
DANN	Benign	0.50
PhyloP100		-1.2
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: rs7863451; hg19: chr9-130072244;