rs1147707

Variant names:

• chr3-120450401-C-T
• rs1147707
• NM_007085.5:c.63+283G>A

Variant summary

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

The NM_007085.5(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 NM_007085.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.552
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FSTL1	NM_007085.5	c.63+283G>A		intron_variant	Intron 2 of 10	ENST00000295633.8	NP_009016.1
LOC124900546	XR_007096030.1	n.254G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FSTL1	ENST00000295633.8	c.63+283G>A		intron_variant	Intron 2 of 10	1	NM_007085.5	ENSP00000295633.3

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

African (AFR) AF: 0.0939 AC: 3901 AN: 41526

American (AMR) AF: 0.227 AC: 3471 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1140 AN: 3466

East Asian (EAS) AF: 0.205 AC: 1057 AN: 5160

South Asian (SAS) AF: 0.260 AC: 1252 AN: 4824

European-Finnish (FIN) AF: 0.426 AC: 4500 AN: 10562

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26775 AN: 67964

Other (OTH) AF: 0.289 AC: 609 AN: 2110

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
PhyloP100		0.55
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: rs1147707; hg19: chr3-120169248;