6-111720156-T-C

Variant summary

Our verdict is Benign. Variant got -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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

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

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FYN	NM_002037.5	c.-11-94A>G		intron_variant		ENST00000354650.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FYN	ENST00000354650.7	c.-11-94A>G		intron_variant		1	NM_002037.5	P3

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61756 AN: 151970 Hom.: 17098 Cov.: 32

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

Gnomad4 AFR exome AF: 0.803

Gnomad4 AMR exome AF: 0.297

Gnomad4 ASJ exome AF: 0.313

Gnomad4 EAS exome AF: 0.420

Gnomad4 SAS exome AF: 0.465

Gnomad4 FIN exome AF: 0.161

Gnomad4 NFE exome AF: 0.237

Gnomad4 OTH exome AF: 0.309

GnomAD4 genome AF: 0.407 AC: 61876 AN: 152088 Hom.: 17153 Cov.: 32 AF XY: 0.405 AC XY: 30076 AN XY: 74352

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.366

Alfa AF: 0.269 Hom.: 12404

Bravo AF: 0.428

Asia WGS AF: 0.481 AC: 1672 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	1.5
Dann	Benign	0.26

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

LitVar

Other links and lift over

dbSNP: rs706895; hg19: chr6-112041359;