chr5-39119459-T-C

Position:

• chr5-39119459-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001465.6(FYB1):​c.2238+76A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 1,068,180 control chromosomes in the GnomAD database, including 439,069 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.86 (56310 hom., cov: 33)
  • Exomes 𝑓: 0.91 (382759 hom.)
• Consequence: FYB1 NM_001465.6 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.431

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 5-39119459-T-C is Benign according to our data. Variant chr5-39119459-T-C is described in ClinVar as [Benign]. Clinvar id is 1255116.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FYB1	NM_001465.6	c.2238+76A>G		intron_variant		ENST00000512982.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FYB1	ENST00000512982.4	c.2238+76A>G		intron_variant		2	NM_001465.6	P4

Frequencies

GnomAD3 genomes AF: 0.855 AC: 129848 AN: 151824 Hom.: 56295 Cov.: 33

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.863

GnomAD4 exome AF: 0.911 AC: 835128 AN: 916244 Hom.: 382759 AF XY: 0.912 AC XY: 415136 AN XY: 455306

Gnomad4 AFR exome AF: 0.714

Gnomad4 AMR exome AF: 0.878

Gnomad4 ASJ exome AF: 0.925

Gnomad4 EAS exome AF: 0.614

Gnomad4 SAS exome AF: 0.884

Gnomad4 FIN exome AF: 0.925

Gnomad4 NFE exome AF: 0.930

Gnomad4 OTH exome AF: 0.888

GnomAD4 genome AF: 0.855 AC: 129906 AN: 151936 Hom.: 56310 Cov.: 33 AF XY: 0.855 AC XY: 63473 AN XY: 74274

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.932

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.924

Gnomad4 NFE AF: 0.930

Gnomad4 OTH AF: 0.860

Alfa AF: 0.893 Hom.: 7595

Bravo AF: 0.843

Asia WGS AF: 0.744 AC: 2542 AN: 3412

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

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	5.7
DANN	Benign	0.35

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: rs394930; hg19: chr5-39119561; COSMIC: COSV60943243;