1-50444313-G-A

Variant names:

• chr1-50444313-G-A
• rs17106184
• NM_007051.3:c.1870-2790C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007051.3(FAF1):​c.1870-2790C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0843 in 152,264 control chromosomes in the GnomAD database, including 575 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 0.084 (575 hom., cov: 32)
• Consequence: FAF1 NM_007051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 56 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]

FAF1-AS1 (HGNC:40228): (FAF1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.09 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.1870-2790C>T		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.1870-2790C>T		intron	N/A	ENSP00000379457.2
	FAF1	ENST00000494400.5	TSL:2	n.*294-2790C>T		intron	N/A	ENSP00000434929.1
	FAF1-AS1	ENST00000754098.1		n.310-4194G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0843 AC: 12822 AN: 152144 Hom.: 572 Cov.: 32

Gnomad AFR AF: 0.0843

Gnomad AMI AF: 0.0593

Gnomad AMR AF: 0.0670

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0924

Gnomad SAS AF: 0.0609

Gnomad FIN AF: 0.0452

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0919

Gnomad OTH AF: 0.0781

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

GnomAD4 genome AF: 0.0843 AC: 12834 AN: 152264 Hom.: 575 Cov.: 32 AF XY: 0.0815 AC XY: 6066 AN XY: 74462

African (AFR) AF: 0.0842 AC: 3498 AN: 41538

American (AMR) AF: 0.0669 AC: 1023 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 571 AN: 3472

East Asian (EAS) AF: 0.0923 AC: 478 AN: 5180

South Asian (SAS) AF: 0.0607 AC: 293 AN: 4824

European-Finnish (FIN) AF: 0.0452 AC: 480 AN: 10616

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0919 AC: 6250 AN: 68022

Other (OTH) AF: 0.0825 AC: 174 AN: 2110

Alfa AF: 0.0918 Hom.: 1225

Bravo AF: 0.0876

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.66
PhyloP100		-0.031
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: rs17106184; hg19: chr1-50909985;