Variant chr5-39108220-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001465.6(FYB1):c.2467+11T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.883 in 1,516,690 control chromosomes in the GnomAD database, including 591,946 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.87 ( 57179 hom., cov: 31)

Exomes 𝑓: 0.88 ( 534767 hom. )

Consequence

FYB1
NM_001465.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.700

Variant links:

Genes affected

FYB1 (HGNC:4036): (FYN binding protein 1) The protein encoded by this gene is an adapter for the FYN protein and LCP2 signaling cascades in T-cells. The encoded protein is involved in platelet activation and controls the expression of interleukin-2. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2011]

FYB1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 5-39108220-A-G is Benign according to our data. Variant chr5-39108220-A-G is described in ClinVar as [Benign]. Clinvar id is 1267008.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FYB1	NM_001465.6 linkuse as main transcript	c.2467+11T>C		intron_variant		ENST00000512982.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FYB1	ENST00000512982.4 linkuse as main transcript	c.2467+11T>C		intron_variant		2	NM_001465.6	P4	O15117-2

Frequencies

GnomAD3 genomes

AF:

0.866

AC:

131551

AN:

151836

Hom.:

57146

Cov.:

show subpopulations

Gnomad AFR

AF:

0.815

Gnomad AMI

AF:

0.897

Gnomad AMR

AF:

0.835

Gnomad ASJ

AF:

0.938

Gnomad EAS

AF:

0.833

Gnomad SAS

AF:

0.953

Gnomad FIN

AF:

0.945

Gnomad MID

AF:

0.880

Gnomad NFE

AF:

0.884

Gnomad OTH

AF:

0.871

GnomAD3 exomes

AF:

0.881

AC:

137418

AN:

155994

Hom.:

60820

AF XY:

0.889

AC XY:

73116

AN XY:

82282

show subpopulations

Gnomad AFR exome

AF:

0.817

Gnomad AMR exome

AF:

0.795

Gnomad ASJ exome

AF:

0.937

Gnomad EAS exome

AF:

0.817

Gnomad SAS exome

AF:

0.955

Gnomad FIN exome

AF:

0.939

Gnomad NFE exome

AF:

0.883

Gnomad OTH exome

AF:

0.881

GnomAD4 exome

AF:

0.884

AC:

1206871

AN:

1364736

Hom.:

534767

Cov.:

AF XY:

0.887

AC XY:

597493

AN XY:

673706

show subpopulations

Gnomad4 AFR exome

AF:

0.811

Gnomad4 AMR exome

AF:

0.799

Gnomad4 ASJ exome

AF:

0.937

Gnomad4 EAS exome

AF:

0.857

Gnomad4 SAS exome

AF:

0.955

Gnomad4 FIN exome

AF:

0.937

Gnomad4 NFE exome

AF:

0.881

Gnomad4 OTH exome

AF:

0.883

GnomAD4 genome

AF:

0.866

AC:

131637

AN:

151954

Hom.:

57179

Cov.:

AF XY:

0.871

AC XY:

64732

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.815

Gnomad4 AMR

AF:

0.835

Gnomad4 ASJ

AF:

0.938

Gnomad4 EAS

AF:

0.834

Gnomad4 SAS

AF:

0.953

Gnomad4 FIN

AF:

0.945

Gnomad4 NFE

AF:

0.884

Gnomad4 OTH

AF:

0.873

Alfa

AF:

0.876

Hom.:

12484

Bravo

AF:

0.851

Asia WGS

AF:

0.897

AC:

3113

AN:

3472

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 11, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.023

DANN

Benign

0.65

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

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