chr6-111817679-G-A

Variant names:

• chr6-111817679-G-A
• rs2182644
• NM_002037.5:c.-82+28910C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 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=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002037.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FYN	NM_002037.5	MANE Select	c.-82+28910C>T		intron	N/A	NP_002028.1
	FYN	NM_153047.4		c.-82+28910C>T		intron	N/A	NP_694592.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FYN	ENST00000354650.7	TSL:1 MANE Select	c.-82+28910C>T		intron	N/A	ENSP00000346671.3
	FYN	ENST00000912320.1		c.-82+28910C>T		intron	N/A	ENSP00000582379.1
	FYN	ENST00000912326.1		c.-82+936C>T		intron	N/A	ENSP00000582385.1

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

African (AFR) AF: 0.580 AC: 24026 AN: 41422

American (AMR) AF: 0.181 AC: 2765 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 492 AN: 3464

East Asian (EAS) AF: 0.143 AC: 741 AN: 5174

South Asian (SAS) AF: 0.135 AC: 649 AN: 4814

European-Finnish (FIN) AF: 0.0499 AC: 528 AN: 10588

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0996 AC: 6771 AN: 67992

Other (OTH) AF: 0.235 AC: 496 AN: 2110

Alfa AF: 0.139 Hom.: 4903

Bravo AF: 0.266

Asia WGS AF: 0.147 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	15
DANN	Benign	0.67
PhyloP100		2.4
Mutation Taster		=99/1	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: rs2182644; hg19: chr6-112138882;