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GeneBe

rs9400504

Variant summary

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

The NM_002037.5(FYN):c.-81-4454G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 152,022 control chromosomes in the GnomAD database, including 14,971 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 0.44 ( 14971 hom., cov: 32)

Consequence

FYN
NM_002037.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.52
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]

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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=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FYNNM_002037.5 linkuse as main transcriptc.-81-4454G>A intron_variant ENST00000354650.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FYNENST00000354650.7 linkuse as main transcriptc.-81-4454G>A intron_variant 1 NM_002037.5 P3P06241-1

Frequencies

GnomAD3 genomes
AF:
0.439
AC:
66654
AN:
151904
Hom.:
14979
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.378
Gnomad AMI
AF:
0.287
Gnomad AMR
AF:
0.555
Gnomad ASJ
AF:
0.425
Gnomad EAS
AF:
0.696
Gnomad SAS
AF:
0.509
Gnomad FIN
AF:
0.412
Gnomad MID
AF:
0.500
Gnomad NFE
AF:
0.430
Gnomad OTH
AF:
0.499
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.439
AC:
66669
AN:
152022
Hom.:
14971
Cov.:
32
AF XY:
0.443
AC XY:
32884
AN XY:
74292
show subpopulations
Gnomad4 AFR
AF:
0.377
Gnomad4 AMR
AF:
0.556
Gnomad4 ASJ
AF:
0.425
Gnomad4 EAS
AF:
0.696
Gnomad4 SAS
AF:
0.508
Gnomad4 FIN
AF:
0.412
Gnomad4 NFE
AF:
0.430
Gnomad4 OTH
AF:
0.493
Alfa
AF:
0.423
Hom.:
3085
Bravo
AF:
0.451
Asia WGS
AF:
0.544
AC:
1894
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
0.12
Dann
Benign
0.36

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: rs9400504; hg19: chr6-112106292; API