rs17059400

Variant names:

• chr6-99335003-A-C
• rs17059400
• NM_032511.4:c.403-1456T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032511.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAXC	NM_032511.4	MANE Select	c.403-1456T>G		intron	N/A	NP_115900.1
	FAXC	NM_001346531.2		c.244-1456T>G		intron	N/A	NP_001333460.1
	FAXC	NM_001346532.1		c.244-1456T>G		intron	N/A	NP_001333461.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAXC	ENST00000389677.6	TSL:1 MANE Select	c.403-1456T>G		intron	N/A	ENSP00000374328.4
	FAXC	ENST00000538471.1	TSL:1	c.-18+7895T>G		intron	N/A	ENSP00000445267.1
	FAXC	ENST00000480148.1	TSL:3	n.306-1456T>G		intron	N/A

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

African (AFR) AF: 0.201 AC: 8359 AN: 41484

American (AMR) AF: 0.221 AC: 3379 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 416 AN: 3470

East Asian (EAS) AF: 0.278 AC: 1431 AN: 5146

South Asian (SAS) AF: 0.278 AC: 1339 AN: 4812

European-Finnish (FIN) AF: 0.0482 AC: 512 AN: 10618

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0653 AC: 4440 AN: 67998

Other (OTH) AF: 0.127 AC: 267 AN: 2110

Alfa AF: 0.0964 Hom.: 2214

Bravo AF: 0.151

Asia WGS AF: 0.298 AC: 1037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.62
PhyloP100		0.40
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: rs17059400; hg19: chr6-99782879; COSMIC: COSV107501079;