rs11205768

Positions:

• chr1-50754455-T-C

Variant summary

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

The NM_007051.3(FAF1):​c.368-9680A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,992 control chromosomes in the GnomAD database, including 18,765 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 0.47 (18765 hom., cov: 31)
• Consequence: FAF1 NM_007051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAF1	NM_007051.3	c.368-9680A>G		intron_variant		ENST00000396153.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAF1	ENST00000396153.7	c.368-9680A>G		intron_variant		1	NM_007051.3	P1
FAF1	ENST00000487898.1	n.390-9680A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71056 AN: 151874 Hom.: 18712 Cov.: 31

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.468 AC: 71156 AN: 151992 Hom.: 18765 Cov.: 31 AF XY: 0.456 AC XY: 33857 AN XY: 74250

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.488

Alfa AF: 0.429 Hom.: 24717

Bravo AF: 0.488

Asia WGS AF: 0.329 AC: 1142 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.29

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: rs11205768; hg19: chr1-51220127;