chr5-39107781-A-G

Position:

• chr5-39107781-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001465.6(FYB1):​c.2468-316T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 151,878 control chromosomes in the GnomAD database, including 41,436 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.73 (41436 hom., cov: 31)
• Consequence: FYB1 NM_001465.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.86

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP6: Variant 5-39107781-A-G is Benign according to our data. Variant chr5-39107781-A-G is described in ClinVar as [Benign]. Clinvar id is 1232537.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FYB1	NM_001465.6	c.2468-316T>C		intron_variant		ENST00000512982.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FYB1	ENST00000512982.4	c.2468-316T>C		intron_variant		2	NM_001465.6	P4

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111493 AN: 151760 Hom.: 41410 Cov.: 31

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.740

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.735 AC: 111574 AN: 151878 Hom.: 41436 Cov.: 31 AF XY: 0.737 AC XY: 54763 AN XY: 74258

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.820

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.822

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.780

Gnomad4 OTH AF: 0.737

Alfa AF: 0.757 Hom.: 5156

Bravo AF: 0.724

Asia WGS AF: 0.697 AC: 2410 AN: 3456

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

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	-0.97
CADD	Benign	0.0020
DANN	Benign	0.30

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

Other links and lift over

dbSNP: rs382753; hg19: chr5-39107883;