1-56721687-C-G

Variant names:

• chr1-56721687-C-G
• rs1342514
• NM_001004303.5:c.1975-1358G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001004303.5(FYB2):​c.1975-1358G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,948 control chromosomes in the GnomAD database, including 7,660 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 (7660 hom., cov: 32)
• Consequence: FYB2 NM_001004303.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.663
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FYB2	NM_001004303.5	c.1975-1358G>C		intron_variant	Intron 17 of 19	ENST00000343433.7	NP_001004303.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FYB2	ENST00000343433.7	c.1975-1358G>C		intron_variant	Intron 17 of 19	1	NM_001004303.5	ENSP00000345972.6
FYB2	ENST00000493000.5	n.892-1358G>C		intron_variant	Intron 11 of 13	5

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46874 AN: 151828 Hom.: 7652 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.309 AC: 46902 AN: 151948 Hom.: 7660 Cov.: 32 AF XY: 0.310 AC XY: 23032 AN XY: 74254

African (AFR) AF: 0.229 AC: 9488 AN: 41466

American (AMR) AF: 0.479 AC: 7289 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1280 AN: 3464

East Asian (EAS) AF: 0.231 AC: 1188 AN: 5150

South Asian (SAS) AF: 0.368 AC: 1774 AN: 4822

European-Finnish (FIN) AF: 0.294 AC: 3110 AN: 10580

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.320 AC: 21725 AN: 67938

Other (OTH) AF: 0.334 AC: 706 AN: 2112

Alfa AF: 0.171 Hom.: 344

Bravo AF: 0.323

Asia WGS AF: 0.311 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.81
DANN	Benign	0.44
PhyloP100		-0.66
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: rs1342514; hg19: chr1-57187360;