rs17059400

Positions:

• chr6-99335003-A-C

Variant summary

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

The NM_032511.4(FAXC):​c.403-1456T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,120 control chromosomes in the GnomAD database, including 1,854 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 0.13 (1854 hom., cov: 32)
• Consequence: FAXC NM_032511.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401

Genes affected

FAXC (HGNC:20742): (failed axon connections homolog, metaxin like GST domain containing) Predicted to be integral component of membrane. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

FAXC (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAXC	NM_032511.4	c.403-1456T>G		intron_variant		ENST00000389677.6	NP_115900.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAXC	ENST00000389677.6	c.403-1456T>G		intron_variant		1	NM_032511.4	ENSP00000374328.4
FAXC	ENST00000538471.1	c.-18+7895T>G		intron_variant		1		ENSP00000445267.1
FAXC	ENST00000480148.1	n.306-1456T>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20223 AN: 151998 Hom.: 1842 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.0482

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.0653

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.133 AC: 20270 AN: 152120 Hom.: 1854 Cov.: 32 AF XY: 0.137 AC XY: 10154 AN XY: 74364

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.0482

Gnomad4 NFE AF: 0.0653

Gnomad4 OTH AF: 0.127

Alfa AF: 0.0905 Hom.: 1347

Bravo AF: 0.151

Asia WGS AF: 0.298 AC: 1037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.62

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: rs17059400; hg19: chr6-99782879;