rs706909

Variant summary

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

The NM_002037.5(FYN):​c.-11-7024A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,170 control chromosomes in the GnomAD database, including 52,996 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 0.83 ( 52996 hom., cov: 32)

Consequence

FYN
NM_002037.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0320
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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FYNNM_002037.5 linkuse as main transcriptc.-11-7024A>G intron_variant ENST00000354650.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FYNENST00000354650.7 linkuse as main transcriptc.-11-7024A>G intron_variant 1 NM_002037.5 P3P06241-1

Frequencies

GnomAD3 genomes
AF:
0.828
AC:
125853
AN:
152052
Hom.:
52933
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.958
Gnomad AMI
AF:
0.613
Gnomad AMR
AF:
0.876
Gnomad ASJ
AF:
0.802
Gnomad EAS
AF:
0.922
Gnomad SAS
AF:
0.909
Gnomad FIN
AF:
0.675
Gnomad MID
AF:
0.867
Gnomad NFE
AF:
0.751
Gnomad OTH
AF:
0.846
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.828
AC:
125976
AN:
152170
Hom.:
52996
Cov.:
32
AF XY:
0.827
AC XY:
61504
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.959
Gnomad4 AMR
AF:
0.877
Gnomad4 ASJ
AF:
0.802
Gnomad4 EAS
AF:
0.922
Gnomad4 SAS
AF:
0.909
Gnomad4 FIN
AF:
0.675
Gnomad4 NFE
AF:
0.751
Gnomad4 OTH
AF:
0.847
Alfa
AF:
0.787
Hom.:
11216
Bravo
AF:
0.847
Asia WGS
AF:
0.898
AC:
3121
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.1
DANN
Benign
0.35

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: rs706909; hg19: chr6-112048289; COSMIC: COSV57611721; API