rs11382443

chr12-95109193-T-TA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_018351.4(FGD6):c.3134-633_3134-632insT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,018 control chromosomes in the GnomAD database, including 6,996 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (6996 hom., cov: 18)
• Consequence: FGD6 NM_018351.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

Genes affected

FGD6 (HGNC:21740): (FYVE, RhoGEF and PH domain containing 6) Predicted to enable guanyl-nucleotide exchange factor activity and small GTPase binding activity. Predicted to be involved in several processes, including filopodium assembly; regulation of GTPase activity; and regulation of cell shape. Predicted to be located in Golgi apparatus; lamellipodium; and ruffle. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGD6	NM_018351.4	c.3134-633_3134-632insT		intron_variant		ENST00000343958.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGD6	ENST00000343958.9	c.3134-633_3134-632insT		intron_variant		1	NM_018351.4	P1

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44899 AN: 151896 Hom.: 6985 Cov.: 18

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.296 AC: 44923 AN: 152018 Hom.: 6996 Cov.: 18 AF XY: 0.294 AC XY: 21868 AN XY: 74302

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.323

Alfa AF: 0.302 Hom.: 877

Bravo AF: 0.298

Asia WGS AF: 0.337 AC: 1174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs11382443; hg19: chr12-95502969;