rs11205760

Variant names:

• chr1-50708658-C-T
• rs11205760
• NM_007051.3:c.552-2767G>A

Variant summary

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

The NM_007051.3(FAF1):​c.552-2767G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 151,716 control chromosomes in the GnomAD database, including 8,945 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 0.30 (8945 hom., cov: 31)
• Consequence: FAF1 NM_007051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 14 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAF1	NM_007051.3	MANE Select	c.552-2767G>A		intron	N/A	NP_008982.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAF1	ENST00000396153.7	TSL:1 MANE Select	c.552-2767G>A		intron	N/A	ENSP00000379457.2
	FAF1	ENST00000487898.1	TSL:3	n.574-2767G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44812 AN: 151598 Hom.: 8932 Cov.: 31

Gnomad AFR AF: 0.0698

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.295 AC: 44827 AN: 151716 Hom.: 8945 Cov.: 31 AF XY: 0.308 AC XY: 22818 AN XY: 74100

African (AFR) AF: 0.0696 AC: 2879 AN: 41380

American (AMR) AF: 0.451 AC: 6872 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 766 AN: 3466

East Asian (EAS) AF: 0.765 AC: 3933 AN: 5144

South Asian (SAS) AF: 0.306 AC: 1468 AN: 4802

European-Finnish (FIN) AF: 0.509 AC: 5316 AN: 10454

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22601 AN: 67936

Other (OTH) AF: 0.285 AC: 600 AN: 2102

Alfa AF: 0.315 Hom.: 24677

Bravo AF: 0.289

Asia WGS AF: 0.460 AC: 1599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.1
DANN	Benign	0.46
PhyloP100		-0.0090
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: rs11205760; hg19: chr1-51174330;