3-120400632-T-C

Variant names:

• chr3-120400632-T-C
• rs1147696
• NM_007085.5:c.806-673A>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.806-673A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,088 control chromosomes in the GnomAD database, including 14,282 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 0.42 (14282 hom., cov: 32)
• Consequence: FSTL1 NM_007085.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.265
• 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]

BTNL12P (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSTL1	NM_007085.5	c.806-673A>G		intron_variant	Intron 9 of 10	ENST00000295633.8	NP_009016.1
BTNL12P	NR_187254.1	n.997-15169T>C		intron_variant	Intron 3 of 4
BTNL12P	NR_187255.1	n.997-15169T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FSTL1	ENST00000295633.8	c.806-673A>G		intron_variant	Intron 9 of 10	1	NM_007085.5	ENSP00000295633.3

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64259 AN: 151970 Hom.: 14270 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.423 AC: 64313 AN: 152088 Hom.: 14282 Cov.: 32 AF XY: 0.421 AC XY: 31293 AN XY: 74366

African (AFR) AF: 0.349 AC: 14478 AN: 41452

American (AMR) AF: 0.465 AC: 7102 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1409 AN: 3468

East Asian (EAS) AF: 0.0285 AC: 148 AN: 5188

South Asian (SAS) AF: 0.376 AC: 1816 AN: 4824

European-Finnish (FIN) AF: 0.460 AC: 4859 AN: 10572

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33117 AN: 67980

Other (OTH) AF: 0.430 AC: 909 AN: 2112

Alfa AF: 0.462 Hom.: 69745

Bravo AF: 0.421

Asia WGS AF: 0.242 AC: 846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.0
DANN	Benign	0.80
PhyloP100		0.27
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: rs1147696; hg19: chr3-120119479;