rs1147707

Positions:

• chr3-120450401-C-T

Variant summary

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

The ENST00000295633.8(FSTL1):​c.63+283G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,108 control chromosomes in the GnomAD database, including 7,600 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 0.29 (7600 hom., cov: 32)
• Consequence: FSTL1 ENST00000295633.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.552

Genes affected

FSTL1 (HGNC:3972): (follistatin like 1) This gene encodes a protein with similarity to follistatin, an activin-binding protein. It contains an FS module, a follistatin-like sequence containing 10 conserved cysteine residues. This gene product is thought to be an autoantigen associated with rheumatoid arthritis. [provided by RefSeq, Jul 2008]

LOC124900546 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSTL1	NM_007085.5	c.63+283G>A		intron_variant		ENST00000295633.8	NP_009016.1
LOC124900546	XR_007096030.1	n.254G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FSTL1	ENST00000295633.8	c.63+283G>A		intron_variant		1	NM_007085.5	ENSP00000295633	P1
	ENST00000659560.1	n.179+1249C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43361 AN: 151990 Hom.: 7602 Cov.: 32

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.285 AC: 43361 AN: 152108 Hom.: 7600 Cov.: 32 AF XY: 0.283 AC XY: 21052 AN XY: 74344

Gnomad4 AFR AF: 0.0939

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.289

Alfa AF: 0.304 Hom.: 1232

Bravo AF: 0.266

Asia WGS AF: 0.227 AC: 788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	15
DANN	Benign	0.96

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

Publications

LitVar

Other links and lift over

dbSNP: rs1147707; hg19: chr3-120169248;