Genetic Variant FYN:c.-11-94A>G (chr6-111720156-T-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_002037.5(FYN):c.-11-94A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 1,424,162 control chromosomes in the GnomAD database, including 70,761 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 0.41 ( 17153 hom., cov: 32)

Exomes 𝑓: 0.27 ( 53608 hom. )

Consequence

FYN
NM_002037.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.33

Publications

31 publications found

Variant links:

Genes affected

FYN (HGNC:4037): (FYN proto-oncogene, Src family tyrosine kinase) This gene is a member of the protein-tyrosine kinase oncogene family. It encodes a membrane-associated tyrosine kinase that has been implicated in the control of cell growth. The protein associates with the p85 subunit of phosphatidylinositol 3-kinase and interacts with the fyn-binding protein. Alternatively spliced transcript variants encoding distinct isoforms exist. [provided by RefSeq, Jul 2008]

FYN links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002037.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FYN	NM_002037.5	MANE Select	c.-11-94A>G	intron	N/A	NP_002028.1
FYN	NM_001370529.1		c.-11-94A>G	intron	N/A	NP_001357458.1
FYN	NM_153047.4		c.-11-94A>G	intron	N/A	NP_694592.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FYN	ENST00000354650.7	TSL:1 MANE Select	c.-11-94A>G	intron	N/A	ENSP00000346671.3
FYN	ENST00000229471.8	TSL:1	c.-11-94A>G	intron	N/A	ENSP00000229471.4
FYN	ENST00000905552.1		c.-11-94A>G	intron	N/A	ENSP00000575611.1

Frequencies

GnomAD3 genomes

AF:

0.406

AC:

61756

AN:

151970

Hom.:

17098

Cov.:

show subpopulations

Gnomad AFR

AF:

0.783

Gnomad AMI

AF:

0.0691

Gnomad AMR

AF:

0.311

Gnomad ASJ

AF:

0.319

Gnomad EAS

AF:

0.457

Gnomad SAS

AF:

0.471

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.239

Gnomad OTH

AF:

0.361

GnomAD4 exome

AF:

0.270

AC:

342916

AN:

1272074

Hom.:

53608

AF XY:

0.273

AC XY:

169754

AN XY:

621142

show subpopulations

African (AFR)

AF:

0.803

AC:

22919

AN:

28556

American (AMR)

AF:

0.297

AC:

7252

AN:

24428

Ashkenazi Jewish (ASJ)

AF:

0.313

AC:

5962

AN:

19026

East Asian (EAS)

AF:

0.420

AC:

15301

AN:

36456

South Asian (SAS)

AF:

0.465

AC:

29414

AN:

63308

European-Finnish (FIN)

AF:

0.161

AC:

7173

AN:

44528

Middle Eastern (MID)

AF:

0.365

AC:

1872

AN:

5128

European-Non Finnish (NFE)

AF:

0.237

AC:

236622

AN:

997652

Other (OTH)

AF:

0.309

AC:

16401

AN:

52992

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

11221

22443

33664

44886

56107

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8740

17480

26220

34960

43700

<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:

0.407

AC:

61876

AN:

152088

Hom.:

17153

Cov.:

AF XY:

0.405

AC XY:

30076

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.783

AC:

32487

AN:

41468

American (AMR)

AF:

0.311

AC:

4754

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.319

AC:

1106

AN:

3470

East Asian (EAS)

AF:

0.457

AC:

2361

AN:

5166

South Asian (SAS)

AF:

0.471

AC:

2271

AN:

4824

European-Finnish (FIN)

AF:

0.163

AC:

1727

AN:

10584

Middle Eastern (MID)

AF:

0.323

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.239

AC:

16239

AN:

67978

Other (OTH)

AF:

0.366

AC:

773

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1409

2817

4226

5634

7043

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

542

1084

1626

2168

2710

<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:

0.291

Hom.:

33616

Bravo

AF:

0.428

Asia WGS

AF:

0.481

AC:

1672

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.5

(source)

DANN

Benign

0.26

PhyloP100

-1.3

PromoterAI

-0.018

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.40

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.40

Position offset: 0

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