rs1149795

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007051.3(FAF1):​c.1495-15091C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 152,242 control chromosomes in the GnomAD database, including 62,350 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 0.90 ( 62350 hom., cov: 32)

Consequence

FAF1
NM_007051.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.298
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FAF1NM_007051.3 linkuse as main transcriptc.1495-15091C>T intron_variant ENST00000396153.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FAF1ENST00000396153.7 linkuse as main transcriptc.1495-15091C>T intron_variant 1 NM_007051.3 P1Q9UNN5-1
FAF1ENST00000494400.5 linkuse as main transcriptc.913-15091C>T intron_variant, NMD_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.903
AC:
137309
AN:
152124
Hom.:
62274
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.971
Gnomad AMI
AF:
0.924
Gnomad AMR
AF:
0.924
Gnomad ASJ
AF:
0.860
Gnomad EAS
AF:
0.903
Gnomad SAS
AF:
0.692
Gnomad FIN
AF:
0.835
Gnomad MID
AF:
0.864
Gnomad NFE
AF:
0.884
Gnomad OTH
AF:
0.895
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.903
AC:
137444
AN:
152242
Hom.:
62350
Cov.:
32
AF XY:
0.897
AC XY:
66738
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.971
Gnomad4 AMR
AF:
0.924
Gnomad4 ASJ
AF:
0.860
Gnomad4 EAS
AF:
0.902
Gnomad4 SAS
AF:
0.694
Gnomad4 FIN
AF:
0.835
Gnomad4 NFE
AF:
0.884
Gnomad4 OTH
AF:
0.896
Alfa
AF:
0.885
Hom.:
120911
Bravo
AF:
0.919
Asia WGS
AF:
0.811
AC:
2823
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.3
DANN
Benign
0.27

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1149795; hg19: chr1-50972564; COSMIC: COSV65637292; API