chr3-120400632-T-C

Position:

• chr3-120400632-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
FSTL1	NM_007085.5	c.806-673A>G		intron_variant		ENST00000295633.8
LRRC58-DT	XR_007096031.1	n.964-15169T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FSTL1	ENST00000295633.8	c.806-673A>G		intron_variant		1	NM_007085.5	P1
	ENST00000494869.2	n.633-15169T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.0285

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.430

Alfa AF: 0.469 Hom.: 34522

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

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: rs1147696; hg19: chr3-120119479;