rs11205768

Variant names:

• chr1-50754455-T-C
• rs11205768
• NM_007051.3:c.368-9680A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-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 rank	MANE	Protein	UniProt
FAF1	NM_007051.3	c.368-9680A>G		intron_variant	Intron 4 of 18	ENST00000396153.7	NP_008982.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAF1	ENST00000396153.7	c.368-9680A>G		intron_variant	Intron 4 of 18	1	NM_007051.3	ENSP00000379457.2
FAF1	ENST00000487898.1	n.390-9680A>G		intron_variant	Intron 4 of 6	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

African (AFR) AF: 0.705 AC: 29222 AN: 41464

American (AMR) AF: 0.371 AC: 5663 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1905 AN: 3472

East Asian (EAS) AF: 0.171 AC: 879 AN: 5150

South Asian (SAS) AF: 0.345 AC: 1665 AN: 4830

European-Finnish (FIN) AF: 0.234 AC: 2467 AN: 10562

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27843 AN: 67950

Other (OTH) AF: 0.488 AC: 1031 AN: 2112

Alfa AF: 0.443 Hom.: 43447

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
PhyloP100		-1.3
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: rs11205768; hg19: chr1-51220127;