1-56777781-T-C

Position:

• chr1-56777781-T-C

Variant summary

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

The NM_001004303.5(FYB2):​c.953+9394A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,836 control chromosomes in the GnomAD database, including 8,813 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 (8813 hom., cov: 31)
• Consequence: FYB2 NM_001004303.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222

Genes affected

FYB2 (HGNC:27295): (FYN binding protein 2) Involved in T cell receptor signaling pathway and cell adhesion mediated by integrin. Located in immunological synapse and membrane raft. [provided by Alliance of Genome Resources, Apr 2022]

FYB2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FYB2	NM_001004303.5	c.953+9394A>G		intron_variant		ENST00000343433.7	NP_001004303.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FYB2	ENST00000343433.7	c.953+9394A>G		intron_variant		1	NM_001004303.5	ENSP00000345972.6
FYB2	ENST00000484327.1	n.1359+9394A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47390 AN: 151716 Hom.: 8808 Cov.: 31

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.312 AC: 47401 AN: 151836 Hom.: 8813 Cov.: 31 AF XY: 0.310 AC XY: 22994 AN XY: 74188

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.320

Alfa AF: 0.357 Hom.: 5833

Bravo AF: 0.304

Asia WGS AF: 0.264 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.31

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: rs17372114; hg19: chr1-57243454;