chr7-102813856-T-C

Variant names:

• chr7-102813856-T-C
• rs7779121
• ENST00000440067.4:c.2289-325A>G

Variant summary

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

The ENST00000440067.4(FBXL13):​c.2289-325A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,092 control chromosomes in the GnomAD database, including 1,425 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 0.13 (1425 hom., cov: 31)
• Consequence: FBXL13 ENST00000440067.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.692
• Publications: 7 publications found

Genes affected

FBXL13 (HGNC:21658): (F-box and leucine rich repeat protein 13) Members of the F-box protein family, such as FBXL13, are characterized by an approximately 40-amino acid F-box motif. SCF complexes, formed by SKP1 (MIM 601434), cullin (see CUL1; MIM 603134), and F-box proteins, act as protein-ubiquitin ligases. F-box proteins interact with SKP1 through the F box, and they interact with ubiquitination targets through other protein interaction domains (Jin et al., 2004 [PubMed 15520277]).[supplied by OMIM, Mar 2008]

FAM185A (HGNC:22412): (family with sequence similarity 185 member A)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FBXL13	XM_011515929.4	c.*1720A>G		3_prime_UTR_variant	Exon 21 of 21		XP_011514231.1
FBXL13	XM_047420043.1	c.*533A>G		3_prime_UTR_variant	Exon 21 of 21		XP_047275999.1
FBXL13	NM_001394494.2	c.2289-325A>G		intron_variant	Intron 20 of 20		NP_001381423.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBXL13	ENST00000440067.4	c.2289-325A>G		intron_variant	Intron 20 of 20	3		ENSP00000390126.2

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19164 AN: 151974 Hom.: 1427 Cov.: 31

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.0801

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0930

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.126 AC: 19185 AN: 152092 Hom.: 1425 Cov.: 31 AF XY: 0.130 AC XY: 9638 AN XY: 74344

African (AFR) AF: 0.166 AC: 6877 AN: 41484

American (AMR) AF: 0.0801 AC: 1224 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 390 AN: 3470

East Asian (EAS) AF: 0.305 AC: 1572 AN: 5150

South Asian (SAS) AF: 0.240 AC: 1154 AN: 4802

European-Finnish (FIN) AF: 0.112 AC: 1186 AN: 10592

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0930 AC: 6324 AN: 67998

Other (OTH) AF: 0.104 AC: 220 AN: 2110

Alfa AF: 0.103 Hom.: 1467

Bravo AF: 0.126

Asia WGS AF: 0.277 AC: 959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.0
DANN	Benign	0.68
PhyloP100		0.69
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: rs7779121; hg19: chr7-102454303;