chr6-111713799-A-G

Variant names:

• chr6-111713799-A-G
• rs809192
• NM_002037.5:c.344+548T>C

Variant summary

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

The NM_002037.5(FYN):​c.344+548T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,240 control chromosomes in the GnomAD database, including 52,888 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 (52888 hom., cov: 32)
• Consequence: FYN NM_002037.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FYN	NM_002037.5	c.344+548T>C		intron_variant	Intron 5 of 13	ENST00000354650.7	NP_002028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FYN	ENST00000354650.7	c.344+548T>C		intron_variant	Intron 5 of 13	1	NM_002037.5	ENSP00000346671.3

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125769 AN: 152122 Hom.: 52824 Cov.: 32

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.844

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.827 AC: 125893 AN: 152240 Hom.: 52888 Cov.: 32 AF XY: 0.826 AC XY: 61479 AN XY: 74422

African (AFR) AF: 0.954 AC: 39643 AN: 41572

American (AMR) AF: 0.876 AC: 13412 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2782 AN: 3470

East Asian (EAS) AF: 0.928 AC: 4802 AN: 5176

South Asian (SAS) AF: 0.912 AC: 4400 AN: 4826

European-Finnish (FIN) AF: 0.675 AC: 7127 AN: 10560

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

European-Non Finnish (NFE) AF: 0.752 AC: 51128 AN: 68010

Other (OTH) AF: 0.845 AC: 1787 AN: 2114

Alfa AF: 0.782 Hom.: 210108

Bravo AF: 0.845

Asia WGS AF: 0.900 AC: 3128 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	3.5
DANN	Benign	0.49
PhyloP100		0.14
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: rs809192; hg19: chr6-112035002;