rs16635

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-99341898-AATG-A
• chr6-99341898-AATG-AATGATG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_032511.4(FAXC):​c.402+997_402+999delCAT 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: 𝑓 0.49 (18798 hom., 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: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAXC	NM_032511.4	MANE Select	c.402+997_402+999delCAT		intron	N/A	NP_115900.1	Q5TGI0-1
	FAXC	NM_001346531.2		c.243+997_243+999delCAT		intron	N/A	NP_001333460.1
	FAXC	NM_001346532.1		c.243+997_243+999delCAT		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+997_402+999delCAT		intron	N/A	ENSP00000374328.4	Q5TGI0-1
	FAXC	ENST00000538471.1	TSL:1	c.-18+997_-18+999delCAT		intron	N/A	ENSP00000445267.1	Q5TGI0-2
	FAXC	ENST00000480148.1	TSL:3	n.305+997_305+999delCAT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74947 AN: 151626 Hom.: 18787 Cov.: 0

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.494 AC: 74978 AN: 151744 Hom.: 18798 Cov.: 0 AF XY: 0.489 AC XY: 36296 AN XY: 74162

African (AFR) AF: 0.566 AC: 23407 AN: 41324

American (AMR) AF: 0.337 AC: 5141 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1718 AN: 3468

East Asian (EAS) AF: 0.596 AC: 3064 AN: 5140

South Asian (SAS) AF: 0.412 AC: 1985 AN: 4822

European-Finnish (FIN) AF: 0.488 AC: 5141 AN: 10536

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.485 AC: 32921 AN: 67876

Other (OTH) AF: 0.500 AC: 1053 AN: 2104

Alfa AF: 0.502 Hom.: 2358

Bravo AF: 0.490

Asia WGS AF: 0.428 AC: 1489 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.4
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: rs16635; hg19: chr6-99789774;