6-99341898-AATG-AATGATG

Variant names:

• chr6-99341898-A-AATG
• rs16635
• NM_032511.4:c.402+997_402+999dupCAT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_032511.4(FAXC):​c.402+997_402+999dupCAT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: FAXC NM_032511.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• Publications: 3 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: Uncertain_significance. The variant received 0 ACMG points.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAXC	NM_032511.4	MANE Select	c.402+997_402+999dupCAT		intron	N/A	NP_115900.1	Q5TGI0-1
	FAXC	NM_001346531.2		c.243+997_243+999dupCAT		intron	N/A	NP_001333460.1
	FAXC	NM_001346532.1		c.243+997_243+999dupCAT		intron	N/A	NP_001333461.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAXC	ENST00000389677.6	TSL:1 MANE Select	c.402+999_402+1000insCAT		intron	N/A	ENSP00000374328.4	Q5TGI0-1
	FAXC	ENST00000538471.1	TSL:1	c.-18+999_-18+1000insCAT		intron	N/A	ENSP00000445267.1	Q5TGI0-2
	FAXC	ENST00000480148.1	TSL:3	n.305+999_305+1000insCAT		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs16635; hg19: chr6-99789774;