Variant chr6-111694367-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_002037.5(FYN):c.1273+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00714 in 1,613,986 control chromosomes in the GnomAD database, including 47 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0045 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0074 ( 46 hom. )

Consequence

FYN
NM_002037.5 splice_region, intron

Scores

Splicing: ADA: 0.04223

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.212

Variant links:

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 links:

LOC105377945 (HGNC:):

LOC105377945 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

Variant 6-111694367-G-A is Benign according to our data. Variant chr6-111694367-G-A is described in ClinVar as [Benign]. Clinvar id is 768108.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 680 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FYN	NM_002037.5 linkuse as main transcript	c.1273+8C>T		splice_region_variant, intron_variant		ENST00000354650.7	NP_002028.1
LOC105377945	XR_001743812.2 linkuse as main transcript	n.760G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FYN	ENST00000354650.7 linkuse as main transcript	c.1273+8C>T		splice_region_variant, intron_variant		1	NM_002037.5	ENSP00000346671	P3	P06241-1

Frequencies

GnomAD3 genomes

AF:

0.00447

AC:

681

AN:

152216

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00116

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00242

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00663

Gnomad FIN

AF:

0.00188

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00776

Gnomad OTH

AF:

0.00430

GnomAD3 exomes

AF:

0.00558

AC:

1402

AN:

251142

Hom.:

AF XY:

0.00604

AC XY:

819

AN XY:

135708

show subpopulations

Gnomad AFR exome

AF:

0.00129

Gnomad AMR exome

AF:

0.00217

Gnomad ASJ exome

AF:

0.00169

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00700

Gnomad FIN exome

AF:

0.00231

Gnomad NFE exome

AF:

0.00881

Gnomad OTH exome

AF:

0.00408

GnomAD4 exome

AF:

0.00742

AC:

10850

AN:

1461652

Hom.:

Cov.:

AF XY:

0.00734

AC XY:

5335

AN XY:

727106

show subpopulations

Gnomad4 AFR exome

AF:

0.00102

Gnomad4 AMR exome

AF:

0.00201

Gnomad4 ASJ exome

AF:

0.00138

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00690

Gnomad4 FIN exome

AF:

0.00264

Gnomad4 NFE exome

AF:

0.00859

Gnomad4 OTH exome

AF:

0.00633

GnomAD4 genome

AF:

0.00446

AC:

680

AN:

152334

Hom.:

Cov.:

AF XY:

0.00403

AC XY:

300

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.00115

Gnomad4 AMR

AF:

0.00242

Gnomad4 ASJ

AF:

0.00144

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00643

Gnomad4 FIN

AF:

0.00188

Gnomad4 NFE

AF:

0.00776

Gnomad4 OTH

AF:

0.00426

Alfa

AF:

0.00625

Hom.:

Bravo

AF:

0.00433

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.00676

EpiControl

AF:

0.00741

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 15, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

6.4

DANN

Benign

0.79

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.042

dbscSNV1_RF

Benign

0.14

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over