chr1-50611150-G-A

Position:

• chr1-50611150-G-A

Variant summary

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

The NM_007051.3(FAF1):​c.745-14934C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0918 in 152,190 control chromosomes in the GnomAD database, including 822 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 0.092 (822 hom., cov: 33)
• Consequence: FAF1 NM_007051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

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=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAF1	NM_007051.3	c.745-14934C>T		intron_variant		ENST00000396153.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAF1	ENST00000396153.7	c.745-14934C>T		intron_variant		1	NM_007051.3	P1
FAF1	ENST00000494400.5	c.163-14934C>T		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0917 AC: 13945 AN: 152072 Hom.: 818 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0605

Gnomad ASJ AF: 0.0521

Gnomad EAS AF: 0.0727

Gnomad SAS AF: 0.0452

Gnomad FIN AF: 0.0400

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0918 AC: 13971 AN: 152190 Hom.: 822 Cov.: 33 AF XY: 0.0898 AC XY: 6682 AN XY: 74422

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0604

Gnomad4 ASJ AF: 0.0521

Gnomad4 EAS AF: 0.0727

Gnomad4 SAS AF: 0.0456

Gnomad4 FIN AF: 0.0400

Gnomad4 NFE AF: 0.0670

Gnomad4 OTH AF: 0.0752

Alfa AF: 0.0893 Hom.: 121

Bravo AF: 0.0967

Asia WGS AF: 0.0690 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	3.9
DANN	Benign	0.43

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: rs12568008; hg19: chr1-51076822;