rs2161612

chr5-39106998-A-G

Variant summary

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

The NM_001465.6(FYB1):c.*445T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,110 control chromosomes in the GnomAD database, including 8,142 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 0.31 (8127 hom., cov: 32)
  • Exomes 𝑓: 0.33 (15 hom.)
• Consequence: FYB1 NM_001465.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FYB1	NM_001465.6	c.*445T>C		3_prime_UTR_variant	19/19	ENST00000512982.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FYB1	ENST00000512982.4	c.*445T>C		3_prime_UTR_variant	19/19	2	NM_001465.6	P4
FYB1	ENST00000351578.12	c.*445T>C		3_prime_UTR_variant	18/18	1		A2
FYB1	ENST00000646045.2	c.*445T>C		3_prime_UTR_variant	19/19			A1

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47017 AN: 151780 Hom.: 8129 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.286

GnomAD4 exome AF: 0.330 AC: 70 AN: 212 Hom.: 15 Cov.: 0 AF XY: 0.402 AC XY: 45 AN XY: 112

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.167

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.357

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.362

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.310 AC: 47014 AN: 151898 Hom.: 8127 Cov.: 32 AF XY: 0.310 AC XY: 23008 AN XY: 74226

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.283

Alfa AF: 0.363 Hom.: 5948

Bravo AF: 0.298

Asia WGS AF: 0.181 AC: 624 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.9
Dann	Benign	0.75

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: rs2161612; hg19: chr5-39107100;