rs16635

Positions:

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

Variant summary

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

The NM_032511.4(FAXC):​c.402+997_402+999del 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

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

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAXC	NM_032511.4	c.402+997_402+999del		intron_variant		ENST00000389677.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAXC	ENST00000389677.6	c.402+997_402+999del		intron_variant		1	NM_032511.4	P1
FAXC	ENST00000538471.1	c.-18+997_-18+999del		intron_variant		1
FAXC	ENST00000480148.1	n.305+997_305+999del		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.500

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 v4.3

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: rs16635; hg19: chr6-99789774;