3-120435334-T-C

Variant names:

• chr3-120435334-T-C
• rs1733302
• NM_007085.5:c.63+15350A>G

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+15350A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,222 control chromosomes in the GnomAD database, including 52,786 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 (52786 hom., cov: 33)
• Consequence: FSTL1 NM_007085.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSTL1	NM_007085.5	c.63+15350A>G		intron_variant	Intron 2 of 10	ENST00000295633.8	NP_009016.1
LOC124900546	XR_007096030.1	n.15321A>G		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+15350A>G		intron_variant	Intron 2 of 10	1	NM_007085.5	ENSP00000295633.3

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125845 AN: 152104 Hom.: 52764 Cov.: 33

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.827 AC: 125919 AN: 152222 Hom.: 52786 Cov.: 33 AF XY: 0.826 AC XY: 61457 AN XY: 74440

African (AFR) AF: 0.713 AC: 29595 AN: 41498

American (AMR) AF: 0.698 AC: 10664 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2615 AN: 3472

East Asian (EAS) AF: 0.923 AC: 4780 AN: 5178

South Asian (SAS) AF: 0.904 AC: 4363 AN: 4826

European-Finnish (FIN) AF: 0.909 AC: 9649 AN: 10610

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.903 AC: 61429 AN: 68028

Other (OTH) AF: 0.816 AC: 1727 AN: 2116

Alfa AF: 0.865 Hom.: 98628

Bravo AF: 0.805

Asia WGS AF: 0.899 AC: 3127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.5
DANN	Benign	0.37
PhyloP100		-0.0060
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: rs1733302; hg19: chr3-120154181;