rs6596140

Positions:

• chr5-133686160-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.-10-82167G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 152,098 control chromosomes in the GnomAD database, including 9,057 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 0.34 (9057 hom., cov: 33)
• Consequence: FSTL4 XM_011543283.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463

Genes affected

FSTL4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSTL4	XM_011543283.2	c.-10-82167G>A		intron_variant			XP_011541585.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52095 AN: 151980 Hom.: 9045 Cov.: 33

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.343 AC: 52143 AN: 152098 Hom.: 9057 Cov.: 33 AF XY: 0.343 AC XY: 25527 AN XY: 74346

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.327

Alfa AF: 0.339 Hom.: 11577

Bravo AF: 0.343

Asia WGS AF: 0.372 AC: 1297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6596140; hg19: chr5-133021851;