rs3862271

chr1-50489324-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007051.3(FAF1):c.1653+1264A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,212 control chromosomes in the GnomAD database, including 5,583 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 0.26 (5583 hom., cov: 33)
• Consequence: FAF1 NM_007051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAF1	NM_007051.3	c.1653+1264A>G		intron_variant		ENST00000396153.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAF1	ENST00000396153.7	c.1653+1264A>G		intron_variant		1	NM_007051.3	P1
FAF1	ENST00000494400.5	c.1071+1264A>G		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39606 AN: 152094 Hom.: 5574 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.260 AC: 39636 AN: 152212 Hom.: 5583 Cov.: 33 AF XY: 0.254 AC XY: 18909 AN XY: 74430

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.311

Alfa AF: 0.281 Hom.: 1249

Bravo AF: 0.261

Asia WGS AF: 0.130 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.5
Dann	Benign	0.58

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: rs3862271; hg19: chr1-50954996;