rs765293776

Variant names:

• chr15-82765286-C-A
• NM_001007122.4:c.1700G>T

Your query was ambiguous. Multiple possible variants found:

• chr15-82765286-C-A
• chr15-82765286-C-G
• chr15-82765286-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001007122.4(FSD2):​c.1700G>T​(p.Arg567Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R567H) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: FSD2 NM_001007122.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349

Genes affected

FSD2 (HGNC:18024): (fibronectin type III and SPRY domain containing 2) This gene encodes a protein that belongs to the FN3/SPRY family of proteins. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.0865967).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSD2	NM_001007122.4	c.1700G>T	p.Arg567Leu	missense_variant	Exon 11 of 13	ENST00000334574.12	NP_001007123.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FSD2	ENST00000334574.12	c.1700G>T	p.Arg567Leu	missense_variant	Exon 11 of 13	1	NM_001007122.4	ENSP00000335651.8
FSD2	ENST00000541889.1	c.1565G>T	p.Arg522Leu	missense_variant	Exon 10 of 12	1		ENSP00000444078.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Benign	-0.50
CADD	Benign	9.4
DANN	Benign	0.65
DEOGEN2	Benign	0.010	T;.
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.21	N
LIST_S2	Uncertain	0.87	D;D
M_CAP	Benign	0.0086	T
MetaRNN	Benign	0.087	T;T
MetaSVM	Benign	-0.94	T
MutationAssessor	Benign	-0.045	N;.
PrimateAI	Benign	0.19	T
PROVEAN	Benign	1.9	N;N
REVEL	Benign	0.080
Sift	Benign	0.74	T;T
Sift4G	Benign	0.17	T;T
Polyphen		0.086	B;.
Vest4		0.34
MutPred		0.70		Gain of methylation at K570 (P = 0.0378);.;
MVP		0.092
MPC		0.063
ClinPred		0.093	T
GERP RS		-3.5
Varity_R		0.062
gMVP		0.38

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr15-83434038;