6-111760532-C-T

Position:

• chr6-111760532-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002037.5(FYN):​c.-12+20034G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,020 control chromosomes in the GnomAD database, including 16,529 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 0.46 (16529 hom., cov: 32)
• Consequence: FYN NM_002037.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360

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]

FYN (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FYN	NM_002037.5	c.-12+20034G>A		intron_variant		ENST00000354650.7	NP_002028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FYN	ENST00000354650.7	c.-12+20034G>A		intron_variant		1	NM_002037.5	ENSP00000346671.3

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70384 AN: 151902 Hom.: 16509 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.463 AC: 70457 AN: 152020 Hom.: 16529 Cov.: 32 AF XY: 0.468 AC XY: 34798 AN XY: 74314

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.515

Alfa AF: 0.443 Hom.: 8043

Bravo AF: 0.475

Asia WGS AF: 0.560 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.60

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

Other links and lift over

dbSNP: rs6914091; hg19: chr6-112081735; COSMIC: COSV57620890; COSMIC: COSV57620890;