rs11587909

chr1-50585127-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAF1	NM_007051.3	c.841-316G>A		intron_variant		ENST00000396153.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAF1	ENST00000396153.7	c.841-316G>A		intron_variant		1	NM_007051.3	P1
FAF1	ENST00000494400.5	c.259-316G>A		intron_variant, NMD_transcript_variant		2
FAF1	ENST00000472808.1	n.195-316G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.296

Alfa AF: 0.270 Hom.: 3120

Bravo AF: 0.241

Asia WGS AF: 0.125 AC: 434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	5.5
Dann	Benign	0.78

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: rs11587909; hg19: chr1-51050799;