rs17106184

chr1-50444313-G-A

Variant summary

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

The NM_007051.3(FAF1):c.1870-2790C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0843 in 152,264 control chromosomes in the GnomAD database, including 575 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 0.084 (575 hom., cov: 32)
• Consequence: FAF1 NM_007051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

Genes affected

FAF1 (HGNC:3578): (Fas associated factor 1) Interaction of Fas ligand (TNFSF6) with the FAS antigen (TNFRSF6) mediates programmed cell death, also called apoptosis, in a number of organ systems. The protein encoded by this gene binds to FAS antigen and can initiate apoptosis or enhance apoptosis initiated through FAS antigen. Initiation of apoptosis by the protein encoded by this gene requires a ubiquitin-like domain but not the FAS-binding domain. [provided by RefSeq, Jul 2008]

FAF1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.09 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAF1	NM_007051.3	c.1870-2790C>T		intron_variant		ENST00000396153.7
FAF1-AS1	XR_007066079.1	n.2826G>A		non_coding_transcript_exon_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAF1	ENST00000396153.7	c.1870-2790C>T		intron_variant		1	NM_007051.3	P1
FAF1	ENST00000494400.5	c.*294-2790C>T		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0843 AC: 12822 AN: 152144 Hom.: 572 Cov.: 32

Gnomad AFR AF: 0.0843

Gnomad AMI AF: 0.0593

Gnomad AMR AF: 0.0670

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0924

Gnomad SAS AF: 0.0609

Gnomad FIN AF: 0.0452

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0919

Gnomad OTH AF: 0.0781

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

GnomAD4 genome AF: 0.0843 AC: 12834 AN: 152264 Hom.: 575 Cov.: 32 AF XY: 0.0815 AC XY: 6066 AN XY: 74462

Gnomad4 AFR AF: 0.0842

Gnomad4 AMR AF: 0.0669

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.0923

Gnomad4 SAS AF: 0.0607

Gnomad4 FIN AF: 0.0452

Gnomad4 NFE AF: 0.0919

Gnomad4 OTH AF: 0.0825

Alfa AF: 0.0826 Hom.: 190

Bravo AF: 0.0876

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.9
Dann	Benign	0.66

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: rs17106184; hg19: chr1-50909985;