rs12568008

Variant names:

• chr1-50611150-G-A
• rs12568008
• NM_007051.3:c.745-14934C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007051.3(FAF1):​c.745-14934C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0918 in 152,190 control chromosomes in the GnomAD database, including 822 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 0.092 (822 hom., cov: 33)
• Consequence: FAF1 NM_007051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007051.3. 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
	FAF1	NM_007051.3	MANE Select	c.745-14934C>T		intron	N/A	NP_008982.1	Q9UNN5-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAF1	ENST00000396153.7	TSL:1 MANE Select	c.745-14934C>T		intron	N/A	ENSP00000379457.2	Q9UNN5-1
	FAF1	ENST00000952059.1		c.745-4208C>T		intron	N/A	ENSP00000622118.1
	FAF1	ENST00000952061.1		c.745-4208C>T		intron	N/A	ENSP00000622120.1

Frequencies

GnomAD3 genomes AF: 0.0917 AC: 13945 AN: 152072 Hom.: 818 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0605

Gnomad ASJ AF: 0.0521

Gnomad EAS AF: 0.0727

Gnomad SAS AF: 0.0452

Gnomad FIN AF: 0.0400

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0918 AC: 13971 AN: 152190 Hom.: 822 Cov.: 33 AF XY: 0.0898 AC XY: 6682 AN XY: 74422

African (AFR) AF: 0.171 AC: 7093 AN: 41500

American (AMR) AF: 0.0604 AC: 924 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0521 AC: 181 AN: 3472

East Asian (EAS) AF: 0.0727 AC: 377 AN: 5184

South Asian (SAS) AF: 0.0456 AC: 220 AN: 4820

European-Finnish (FIN) AF: 0.0400 AC: 424 AN: 10596

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0670 AC: 4556 AN: 68004

Other (OTH) AF: 0.0752 AC: 159 AN: 2114

Alfa AF: 0.0921 Hom.: 131

Bravo AF: 0.0967

Asia WGS AF: 0.0690 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	3.9
DANN	Benign	0.43
PhyloP100		-0.28
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: rs12568008; hg19: chr1-51076822;