5-133712084-T-C

Variant names:

• chr5-133712084-T-C
• rs6596147
• XM_011543283.2:c.-10-108091A>G

Variant summary

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

The XM_011543283.2(FSTL4):​c.-10-108091A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,164 control chromosomes in the GnomAD database, including 53,508 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 0.83 (53508 hom., cov: 31)
• Consequence: FSTL4 XM_011543283.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58
• Publications: 12 publications found

Genes affected

FSTL4 (HGNC:21389): (follistatin like 4) Predicted to enable brain-derived neurotrophic factor binding activity and calcium ion binding activity. Predicted to be involved in cell differentiation. Predicted to act upstream of or within negative regulation of brain-derived neurotrophic factor receptor signaling pathway; negative regulation of collateral sprouting; and negative regulation of dendritic spine development. Predicted to be located in extracellular region and secretory granule. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126887 AN: 152046 Hom.: 53448 Cov.: 31

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.835 AC: 127005 AN: 152164 Hom.: 53508 Cov.: 31 AF XY: 0.836 AC XY: 62184 AN XY: 74398

African (AFR) AF: 0.956 AC: 39694 AN: 41534

American (AMR) AF: 0.835 AC: 12767 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2422 AN: 3472

East Asian (EAS) AF: 0.917 AC: 4745 AN: 5172

South Asian (SAS) AF: 0.776 AC: 3737 AN: 4816

European-Finnish (FIN) AF: 0.828 AC: 8747 AN: 10570

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52243 AN: 68002

Other (OTH) AF: 0.806 AC: 1696 AN: 2104

Alfa AF: 0.784 Hom.: 81119

Bravo AF: 0.841

Asia WGS AF: 0.871 AC: 3029 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.041
DANN	Benign	0.54
PhyloP100		-2.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6596147; hg19: chr5-133047775;