1-50777702-G-C

Variant names:

• chr1-50777702-G-C
• rs1416685
• NM_007051.3:c.367+10298C>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.367+10298C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 150,598 control chromosomes in the GnomAD database, including 15,079 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 0.43 (15079 hom., cov: 27)
• Consequence: FAF1 NM_007051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623
• Publications: 11 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 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.367+10298C>G		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.367+10298C>G		intron	N/A	ENSP00000379457.2
	FAF1	ENST00000487898.1	TSL:3	n.389+10298C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.432 AC: 64969 AN: 150490 Hom.: 15031 Cov.: 27

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.432 AC: 65060 AN: 150598 Hom.: 15079 Cov.: 27 AF XY: 0.422 AC XY: 30996 AN XY: 73498

African (AFR) AF: 0.574 AC: 23455 AN: 40858

American (AMR) AF: 0.359 AC: 5439 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1897 AN: 3462

East Asian (EAS) AF: 0.171 AC: 878 AN: 5132

South Asian (SAS) AF: 0.348 AC: 1659 AN: 4768

European-Finnish (FIN) AF: 0.236 AC: 2418 AN: 10230

Middle Eastern (MID) AF: 0.528 AC: 152 AN: 288

European-Non Finnish (NFE) AF: 0.412 AC: 27866 AN: 67712

Other (OTH) AF: 0.465 AC: 977 AN: 2102

Alfa AF: 0.389 Hom.: 1486

Bravo AF: 0.447

Asia WGS AF: 0.324 AC: 1122 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.093
DANN	Benign	0.45
PhyloP100		-0.62
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: rs1416685; hg19: chr1-51243374;