Variant 5-39108207-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+24T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 1,498,552 control chromosomes in the GnomAD database, including 451,429 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.74 ( 42093 hom., cov: 31)

Exomes 𝑓: 0.78 ( 409336 hom. )

Consequence

FYB1
NM_001465.6 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.169

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 5-39108207-A-G is Benign according to our data. Variant chr5-39108207-A-G is described in ClinVar as [Benign]. Clinvar id is 1230439.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.806 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+24T>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+24T>C		intron_variant		2	NM_001465.6	P4	O15117-2

Frequencies

GnomAD3 genomes

AF:

0.741

AC:

112503

AN:

151744

Hom.:

42066

Cov.:

show subpopulations

Gnomad AFR

AF:

0.650

Gnomad AMI

AF:

0.815

Gnomad AMR

AF:

0.752

Gnomad ASJ

AF:

0.822

Gnomad EAS

AF:

0.618

Gnomad SAS

AF:

0.829

Gnomad FIN

AF:

0.800

Gnomad MID

AF:

0.782

Gnomad NFE

AF:

0.783

Gnomad OTH

AF:

0.748

GnomAD3 exomes

AF:

0.766

AC:

119254

AN:

155678

Hom.:

46090

AF XY:

0.772

AC XY:

63444

AN XY:

82142

show subpopulations

Gnomad AFR exome

AF:

0.655

Gnomad AMR exome

AF:

0.731

Gnomad ASJ exome

AF:

0.823

Gnomad EAS exome

AF:

0.592

Gnomad SAS exome

AF:

0.837

Gnomad FIN exome

AF:

0.794

Gnomad NFE exome

AF:

0.783

Gnomad OTH exome

AF:

0.773

GnomAD4 exome

AF:

0.778

AC:

1047571

AN:

1346690

Hom.:

409336

Cov.:

AF XY:

0.780

AC XY:

519115

AN XY:

665658

show subpopulations

Gnomad4 AFR exome

AF:

0.647

Gnomad4 AMR exome

AF:

0.732

Gnomad4 ASJ exome

AF:

0.815

Gnomad4 EAS exome

AF:

0.641

Gnomad4 SAS exome

AF:

0.836

Gnomad4 FIN exome

AF:

0.795

Gnomad4 NFE exome

AF:

0.782

Gnomad4 OTH exome

AF:

0.767

GnomAD4 genome

AF:

0.741

AC:

112587

AN:

151862

Hom.:

42093

Cov.:

AF XY:

0.745

AC XY:

55273

AN XY:

74222

show subpopulations

Gnomad4 AFR

AF:

0.650

Gnomad4 AMR

AF:

0.752

Gnomad4 ASJ

AF:

0.822

Gnomad4 EAS

AF:

0.618

Gnomad4 SAS

AF:

0.828

Gnomad4 FIN

AF:

0.800

Gnomad4 NFE

AF:

0.783

Gnomad4 OTH

AF:

0.749

Alfa

AF:

0.769

Hom.:

9248

Bravo

AF:

0.731

Asia WGS

AF:

0.769

AC:

2667

AN:

3470

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	Jun 18, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.8

DANN

Benign

0.37

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