rs2182644

chr6-111817679-G-Achr6-111817679-G-C

Variant summary

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

The NM_002037.5(FYN):c.-82+28910C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,030 control chromosomes in the GnomAD database, including 7,783 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 0.24 (7783 hom., cov: 32)
• Consequence: FYN NM_002037.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.44

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=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FYN	NM_002037.5	c.-82+28910C>T		intron_variant		ENST00000354650.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FYN	ENST00000354650.7	c.-82+28910C>T		intron_variant		1	NM_002037.5	P3

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36576 AN: 151912 Hom.: 7770 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0499

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0996

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.241 AC: 36630 AN: 152030 Hom.: 7783 Cov.: 32 AF XY: 0.236 AC XY: 17518 AN XY: 74314

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.0499

Gnomad4 NFE AF: 0.0996

Gnomad4 OTH AF: 0.235

Alfa AF: 0.119 Hom.: 2244

Bravo AF: 0.266

Asia WGS AF: 0.147 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	15
Dann	Benign	0.67

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: rs2182644; hg19: chr6-112138882;