rs706909

Variant names:

• chr6-111727086-T-C
• rs706909
• NM_002037.5:c.-11-7024A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FYN	NM_002037.5	c.-11-7024A>G		intron_variant	Intron 3 of 13	ENST00000354650.7	NP_002028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FYN	ENST00000354650.7	c.-11-7024A>G		intron_variant	Intron 3 of 13	1	NM_002037.5	ENSP00000346671.3

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125853 AN: 152052 Hom.: 52933 Cov.: 32

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

African (AFR) AF: 0.959 AC: 39830 AN: 41554

American (AMR) AF: 0.877 AC: 13403 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2783 AN: 3470

East Asian (EAS) AF: 0.922 AC: 4774 AN: 5180

South Asian (SAS) AF: 0.909 AC: 4384 AN: 4822

European-Finnish (FIN) AF: 0.675 AC: 7122 AN: 10550

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51081 AN: 67994

Other (OTH) AF: 0.847 AC: 1787 AN: 2110

Alfa AF: 0.801 Hom.: 20010

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
PhyloP100		-0.032
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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