chr1-50585127-C-T

Variant names:

• chr1-50585127-C-T
• rs11587909
• NM_007051.3:c.841-316G>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.841-316G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,038 control chromosomes in the GnomAD database, including 4,715 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 0.24 (4715 hom., cov: 32)
• Consequence: FAF1 NM_007051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• Publications: 6 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=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.276 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.841-316G>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.841-316G>A		intron	N/A	ENSP00000379457.2
	FAF1	ENST00000472808.1	TSL:3	n.195-316G>A		intron	N/A
	FAF1	ENST00000494400.5	TSL:2	n.259-316G>A		intron	N/A	ENSP00000434929.1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36301 AN: 151920 Hom.: 4712 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.239 AC: 36315 AN: 152038 Hom.: 4715 Cov.: 32 AF XY: 0.233 AC XY: 17346 AN XY: 74320

African (AFR) AF: 0.203 AC: 8433 AN: 41456

American (AMR) AF: 0.240 AC: 3671 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1250 AN: 3472

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5184

South Asian (SAS) AF: 0.241 AC: 1161 AN: 4814

European-Finnish (FIN) AF: 0.168 AC: 1773 AN: 10560

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19010 AN: 67966

Other (OTH) AF: 0.296 AC: 625 AN: 2110

Alfa AF: 0.269 Hom.: 4143

Bravo AF: 0.241

Asia WGS AF: 0.125 AC: 434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.5
DANN	Benign	0.78
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: rs11587909; hg19: chr1-51050799;