1-50777702-G-C

Variant names:

• chr1-50777702-G-C
• rs1416685
• NM_007051.3:c.367+10298C>G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAF1	NM_007051.3	c.367+10298C>G		intron_variant	Intron 4 of 18	ENST00000396153.7	NP_008982.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAF1	ENST00000396153.7	c.367+10298C>G		intron_variant	Intron 4 of 18	1	NM_007051.3	ENSP00000379457.2
FAF1	ENST00000487898.1	n.389+10298C>G		intron_variant	Intron 4 of 6	3

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

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.465

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.093
DANN	Benign	0.45

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: rs1416685; hg19: chr1-51243374;