rs9327668

Positions:

• chr5-133731114-C-T

Variant summary

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

The XM_011543283.2(FSTL4):​c.-11+110838G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 151,998 control chromosomes in the GnomAD database, including 1,767 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 (1767 hom., cov: 31)
• Consequence: FSTL4 XM_011543283.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416

Genes affected

FSTL4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSTL4	XM_011543283.2	c.-11+110838G>A		intron_variant			XP_011541585.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19292 AN: 151880 Hom.: 1750 Cov.: 31

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.0943

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.0326

Gnomad SAS AF: 0.0437

Gnomad FIN AF: 0.0687

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0839

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.127 AC: 19350 AN: 151998 Hom.: 1767 Cov.: 31 AF XY: 0.126 AC XY: 9324 AN XY: 74286

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.0943

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.0327

Gnomad4 SAS AF: 0.0433

Gnomad4 FIN AF: 0.0687

Gnomad4 NFE AF: 0.0839

Gnomad4 OTH AF: 0.130

Alfa AF: 0.0932 Hom.: 489

Bravo AF: 0.137

Asia WGS AF: 0.0530 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.077
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9327668; hg19: chr5-133066805;