Variant chr5-39110312-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001465.6(FYB1):c.2435+44T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00634 in 1,333,202 control chromosomes in the GnomAD database, including 175 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 51 hom., cov: 32)

Exomes 𝑓: 0.0048 ( 124 hom. )

Consequence

FYB1
NM_001465.6 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.129

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=-0.8).

BP6

Variant 5-39110312-A-T is Benign according to our data. Variant chr5-39110312-A-T is described in ClinVar as [Benign]. Clinvar id is 1256832.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0182 (2764/152170) while in subpopulation EAS AF= 0.0513 (266/5186). AF 95% confidence interval is 0.0493. There are 51 homozygotes in gnomad4. There are 1381 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 51 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FYB1	NM_001465.6 linkuse as main transcript	c.2435+44T>A		intron_variant		ENST00000512982.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FYB1	ENST00000512982.4 linkuse as main transcript	c.2435+44T>A		intron_variant		2	NM_001465.6	P4	O15117-2

Frequencies

GnomAD3 genomes

AF:

0.0182

AC:

2763

AN:

152052

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0512

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00656

Gnomad ASJ

AF:

0.00346

Gnomad EAS

AF:

0.0512

Gnomad SAS

AF:

0.0192

Gnomad FIN

AF:

0.00801

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000868

Gnomad OTH

AF:

0.0129

GnomAD3 exomes

AF:

0.0108

AC:

2312

AN:

214904

Hom.:

AF XY:

0.00981

AC XY:

1151

AN XY:

117288

show subpopulations

Gnomad AFR exome

AF:

0.0514

Gnomad AMR exome

AF:

0.00343

Gnomad ASJ exome

AF:

0.00269

Gnomad EAS exome

AF:

0.0476

Gnomad SAS exome

AF:

0.0166

Gnomad FIN exome

AF:

0.00929

Gnomad NFE exome

AF:

0.00105

Gnomad OTH exome

AF:

0.00930

GnomAD4 exome

AF:

0.00481

AC:

5684

AN:

1181032

Hom.:

124

Cov.:

AF XY:

0.00496

AC XY:

2960

AN XY:

596512

show subpopulations

Gnomad4 AFR exome

AF:

0.0520

Gnomad4 AMR exome

AF:

0.00392

Gnomad4 ASJ exome

AF:

0.00306

Gnomad4 EAS exome

AF:

0.0482

Gnomad4 SAS exome

AF:

0.0163

Gnomad4 FIN exome

AF:

0.00837

Gnomad4 NFE exome

AF:

0.000373

Gnomad4 OTH exome

AF:

0.00862

GnomAD4 genome

AF:

0.0182

AC:

2764

AN:

152170

Hom.:

Cov.:

AF XY:

0.0186

AC XY:

1381

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.0511

Gnomad4 AMR

AF:

0.00656

Gnomad4 ASJ

AF:

0.00346

Gnomad4 EAS

AF:

0.0513

Gnomad4 SAS

AF:

0.0190

Gnomad4 FIN

AF:

0.00801

Gnomad4 NFE

AF:

0.000868

Gnomad4 OTH

AF:

0.0128

Alfa

AF:

0.00916

Hom.:

Bravo

AF:

0.0196

Asia WGS

AF:

0.0350

AC:

120

AN:

3474

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 20, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.1

DANN

Benign

0.78

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