3-120395790-C-T

Variant names:

• chr3-120395790-C-T
• rs1700
• NM_007085.5:c.*1162G>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.*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
• Publications: 30 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]

BTNL12P (HGNC:):

BTNL12P (HGNC:52935): (butyrophilin like 12, pseudogene)

MIR198 (HGNC:31570): (microRNA 198) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007085.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSTL1	NM_007085.5	MANE Select	c.*1162G>A		3_prime_UTR	Exon 11 of 11	NP_009016.1	Q12841-1
	BTNL12P	NR_187254.1		n.997-20011C>T		intron	N/A
	BTNL12P	NR_187255.1		n.997-20011C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSTL1	ENST00000295633.8	TSL:1 MANE Select	c.*1162G>A		3_prime_UTR	Exon 11 of 11	ENSP00000295633.3	Q12841-1
	FSTL1	ENST00000875454.1		c.*1162G>A		3_prime_UTR	Exon 11 of 11	ENSP00000545513.1
	FSTL1	ENST00000955575.1		c.*1162G>A		3_prime_UTR	Exon 10 of 10	ENSP00000625634.1

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

African (AFR) AF: 0.110 AC: 943 AN: 8546

American (AMR) AF: 0.0646 AC: 1853 AN: 28696

Ashkenazi Jewish (ASJ) AF: 0.0828 AC: 886 AN: 10702

East Asian (EAS) AF: 0.00251 AC: 32 AN: 12772

South Asian (SAS) AF: 0.100 AC: 6159 AN: 61454

European-Finnish (FIN) AF: 0.0858 AC: 2628 AN: 30624

Middle Eastern (MID) AF: 0.112 AC: 152 AN: 1360

European-Non Finnish (NFE) AF: 0.111 AC: 20087 AN: 180374

Other (OTH) AF: 0.101 AC: 1546 AN: 15262

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

African (AFR) AF: 0.106 AC: 4385 AN: 41398

American (AMR) AF: 0.0877 AC: 1341 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0920 AC: 319 AN: 3468

East Asian (EAS) AF: 0.00619 AC: 32 AN: 5172

South Asian (SAS) AF: 0.0942 AC: 452 AN: 4798

European-Finnish (FIN) AF: 0.0867 AC: 918 AN: 10586

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7513 AN: 67968

Other (OTH) AF: 0.112 AC: 236 AN: 2106

Alfa AF: 0.103 Hom.: 694

Bravo AF: 0.101

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	7.0
DANN	Benign	0.81
PhyloP100		-0.64
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: rs1700; hg19: chr3-120114637; COSMIC: COSV55233111; COSMIC: COSV55233111;