1-56777781-T-C

Variant names:

• chr1-56777781-T-C
• rs17372114
• NM_001004303.5:c.953+9394A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004303.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FYB2	NM_001004303.5	MANE Select	c.953+9394A>G		intron	N/A	NP_001004303.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FYB2	ENST00000343433.7	TSL:1 MANE Select	c.953+9394A>G		intron	N/A	ENSP00000345972.6	Q5VWT5-1
	FYB2	ENST00000969682.1		c.953+9394A>G		intron	N/A	ENSP00000639741.1
	FYB2	ENST00000867602.1		c.953+9394A>G		intron	N/A	ENSP00000537661.1

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

African (AFR) AF: 0.107 AC: 4417 AN: 41460

American (AMR) AF: 0.374 AC: 5700 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1366 AN: 3468

East Asian (EAS) AF: 0.209 AC: 1078 AN: 5148

South Asian (SAS) AF: 0.258 AC: 1239 AN: 4806

European-Finnish (FIN) AF: 0.406 AC: 4266 AN: 10518

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.416 AC: 28251 AN: 67896

Other (OTH) AF: 0.320 AC: 676 AN: 2110

Alfa AF: 0.369 Hom.: 25831

Bravo AF: 0.304

Asia WGS AF: 0.264 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.31
PhyloP100		-0.22
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17372114; hg19: chr1-57243454;