Genetic Variant NM_007051.3:c.745-16201C>T (chr1-50612417-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_007051.3(FAF1):c.745-16201C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 1,159,192 control chromosomes in the GnomAD database, including 43,174 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 ( 4496 hom., cov: 32)

Exomes 𝑓: 0.28 ( 38678 hom. )

Consequence

FAF1
NM_007051.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.719

Publications

9 publications found

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]

FAF1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.28).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.276 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.745-16201C>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.745-16201C>T		intron	N/A	ENSP00000379457.2
	FAF1	ENST00000494400.5	TSL:2	n.163-16201C>T		intron	N/A	ENSP00000434929.1

Frequencies

GnomAD3 genomes

AF:

0.232

AC:

35213

AN:

152036

Hom.:

4494

Cov.:

show subpopulations

Gnomad AFR

AF:

0.179

Gnomad AMI

AF:

0.272

Gnomad AMR

AF:

0.238

Gnomad ASJ

AF:

0.360

Gnomad EAS

AF:

0.00308

Gnomad SAS

AF:

0.239

Gnomad FIN

AF:

0.167

Gnomad MID

AF:

0.434

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.291

GnomAD4 exome

AF:

0.275

AC:

277207

AN:

1007038

Hom.:

38678

Cov.:

AF XY:

0.275

AC XY:

134283

AN XY:

487526

show subpopulations

African (AFR)

AF:

0.177

AC:

3326

AN:

18824

American (AMR)

AF:

0.214

AC:

1775

AN:

8312

Ashkenazi Jewish (ASJ)

AF:

0.390

AC:

4083

AN:

10460

East Asian (EAS)

AF:

0.00227

AC:

AN:

8380

South Asian (SAS)

AF:

0.263

AC:

13729

AN:

52242

European-Finnish (FIN)

AF:

0.175

AC:

1562

AN:

8926

Middle Eastern (MID)

AF:

0.429

AC:

1667

AN:

3890

European-Non Finnish (NFE)

AF:

0.280

AC:

240945

AN:

860088

Other (OTH)

AF:

0.281

AC:

10101

AN:

35916

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

8984

17968

26951

35935

44919

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9686

19372

29058

38744

48430

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.231

AC:

35213

AN:

152154

Hom.:

4496

Cov.:

AF XY:

0.226

AC XY:

16800

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.178

AC:

7407

AN:

41512

American (AMR)

AF:

0.238

AC:

3634

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.360

AC:

1250

AN:

3472

East Asian (EAS)

AF:

0.00309

AC:

AN:

5186

South Asian (SAS)

AF:

0.240

AC:

1155

AN:

4820

European-Finnish (FIN)

AF:

0.167

AC:

1765

AN:

10588

Middle Eastern (MID)

AF:

0.432

AC:

127

AN:

294

European-Non Finnish (NFE)

AF:

0.279

AC:

18998

AN:

67972

Other (OTH)

AF:

0.290

AC:

613

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1373

2746

4120

5493

6866

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

358

716

1074

1432

1790

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.229

Hom.:

679

Bravo

AF:

0.233

Asia WGS

AF:

0.123

AC:

426

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.28

CADD

Benign

(source)

DANN

Benign

0.87

PhyloP100

0.72

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over