3-120395790-C-T

Position:

• chr3-120395790-C-T

Variant summary

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

The NM_007085.5(FSTL1):​c.*1162G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.099 in 501,774 control chromosomes in the GnomAD database, including 2,668 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 0.10 (826 hom., cov: 31)
  • Exomes 𝑓: 0.098 (1842 hom.)
• Consequence: FSTL1 NM_007085.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642

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]

FSTL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSTL1	NM_007085.5	c.*1162G>A		3_prime_UTR_variant	11/11	ENST00000295633.8	NP_009016.1
BTNL12P	XR_007096031.1	n.964-20011C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FSTL1	ENST00000295633.8	c.*1162G>A		3_prime_UTR_variant	11/11	1	NM_007085.5	ENSP00000295633.3

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15372 AN: 151866 Hom.: 828 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.0879

Gnomad ASJ AF: 0.0920

Gnomad EAS AF: 0.00617

Gnomad SAS AF: 0.0943

Gnomad FIN AF: 0.0867

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.113

GnomAD4 exome AF: 0.0980 AC: 34286 AN: 349790 Hom.: 1842 Cov.: 0 AF XY: 0.0990 AC XY: 19834 AN XY: 200310

Gnomad4 AFR exome AF: 0.110

Gnomad4 AMR exome AF: 0.0646

Gnomad4 ASJ exome AF: 0.0828

Gnomad4 EAS exome AF: 0.00251

Gnomad4 SAS exome AF: 0.100

Gnomad4 FIN exome AF: 0.0858

Gnomad4 NFE exome AF: 0.111

Gnomad4 OTH exome AF: 0.101

GnomAD4 genome AF: 0.101 AC: 15382 AN: 151984 Hom.: 826 Cov.: 31 AF XY: 0.0994 AC XY: 7383 AN XY: 74284

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.0877

Gnomad4 ASJ AF: 0.0920

Gnomad4 EAS AF: 0.00619

Gnomad4 SAS AF: 0.0942

Gnomad4 FIN AF: 0.0867

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.112

Alfa AF: 0.103 Hom.: 357

Bravo AF: 0.101

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	7.0
DANN	Benign	0.81

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: rs1700; hg19: chr3-120114637; COSMIC: COSV55233111; COSMIC: COSV55233111;