rs7768046

Positions:

• chr6-111858729-G-A
• chr6-111858729-G-C
• chr6-111858729-G-T

Variant summary

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

The NM_002037.5(FYN):​c.-122-12100C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 151,684 control chromosomes in the GnomAD database, including 41,364 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 0.72 (41364 hom., cov: 28)
• Consequence: FYN NM_002037.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FYN	NM_002037.5	c.-122-12100C>T		intron_variant		ENST00000354650.7	NP_002028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FYN	ENST00000354650.7	c.-122-12100C>T		intron_variant		1	NM_002037.5	ENSP00000346671	P3

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109183 AN: 151566 Hom.: 41298 Cov.: 28

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.721 AC: 109310 AN: 151684 Hom.: 41364 Cov.: 28 AF XY: 0.722 AC XY: 53458 AN XY: 74052

Gnomad4 AFR AF: 0.934

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.750

Alfa AF: 0.685 Hom.: 8497

Bravo AF: 0.750

Asia WGS AF: 0.854 AC: 2967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	8.0
DANN	Benign	0.49

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: rs7768046; hg19: chr6-112179932;