5-39219513-T-C

Position:

• chr5-39219513-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001465.6(FYB1):​c.-98A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 985,256 control chromosomes in the GnomAD database, including 329,478 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.68 (38068 hom., cov: 32)
  • Exomes 𝑓: 0.83 (291410 hom.)
• Consequence: FYB1 NM_001465.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FYB1	NM_001465.6	c.-98A>G		5_prime_UTR_variant	1/19	ENST00000512982.4	NP_001456.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FYB1	ENST00000512982.4	c.-98A>G		5_prime_UTR_variant	1/19	2	NM_001465.6	ENSP00000425845	P4

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102894 AN: 152004 Hom.: 38061 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.723

GnomAD4 exome AF: 0.832 AC: 693565 AN: 833132 Hom.: 291410 Cov.: 33 AF XY: 0.834 AC XY: 320697 AN XY: 384740

Gnomad4 AFR exome AF: 0.313

Gnomad4 AMR exome AF: 0.740

Gnomad4 ASJ exome AF: 0.821

Gnomad4 EAS exome AF: 0.564

Gnomad4 SAS exome AF: 0.749

Gnomad4 FIN exome AF: 0.849

Gnomad4 NFE exome AF: 0.848

Gnomad4 OTH exome AF: 0.790

GnomAD4 genome AF: 0.677 AC: 102928 AN: 152124 Hom.: 38068 Cov.: 32 AF XY: 0.677 AC XY: 50374 AN XY: 74370

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.736

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.787

Gnomad4 NFE AF: 0.835

Gnomad4 OTH AF: 0.720

Alfa AF: 0.803 Hom.: 48321

Bravo AF: 0.654

Asia WGS AF: 0.614 AC: 2139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.8
DANN	Benign	0.59

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: rs6863066; hg19: chr5-39219615;