rs11587750

Variant names:

• chr1-50685071-G-A
• rs11587750
• NM_007051.3:c.657+20715C>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.657+20715C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,094 control chromosomes in the GnomAD database, including 4,447 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 0.23 (4447 hom., cov: 32)
• Consequence: FAF1 NM_007051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141
• Publications: 7 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAF1	NM_007051.3	c.657+20715C>T		intron_variant	Intron 7 of 18	ENST00000396153.7	NP_008982.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAF1	ENST00000396153.7	c.657+20715C>T		intron_variant	Intron 7 of 18	1	NM_007051.3	ENSP00000379457.2
FAF1	ENST00000494400.5	n.75+20715C>T		intron_variant	Intron 1 of 13	2		ENSP00000434929.1

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35057 AN: 151976 Hom.: 4445 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.230 AC: 35056 AN: 152094 Hom.: 4447 Cov.: 32 AF XY: 0.225 AC XY: 16713 AN XY: 74354

African (AFR) AF: 0.178 AC: 7381 AN: 41506

American (AMR) AF: 0.238 AC: 3634 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1227 AN: 3466

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5188

South Asian (SAS) AF: 0.238 AC: 1144 AN: 4812

European-Finnish (FIN) AF: 0.166 AC: 1762 AN: 10592

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18908 AN: 67940

Other (OTH) AF: 0.288 AC: 608 AN: 2112

Alfa AF: 0.255 Hom.: 2672

Bravo AF: 0.232

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.7
DANN	Benign	0.71
PhyloP100		0.14
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: rs11587750; hg19: chr1-51150743;