rs764053528

Variant names:

• chr4-161386103-C-A
• rs764053528
• NM_020116.5:c.2188G>T

Your query was ambiguous. Multiple possible variants found:

• chr4-161386103-C-A
• chr4-161386103-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_020116.5(FSTL5):​c.2188G>T​(p.Ala730Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/22 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. A730T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: FSTL5 NM_020116.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.86
• Publications: 1 publications found

Genes affected

FSTL5 (HGNC:21386): (follistatin like 5) Predicted to enable calcium ion binding activity. Predicted to be involved in cell differentiation. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000249568 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.15374687).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020116.5. 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
	FSTL5	NM_020116.5	MANE Select	c.2188G>T	p.Ala730Ser	missense	Exon 16 of 16	NP_064501.2	Q8N475-1
	FSTL5	NM_001128427.3		c.2185G>T	p.Ala729Ser	missense	Exon 16 of 16	NP_001121899.1	Q8N475-2
	FSTL5	NM_001128428.3		c.2158G>T	p.Ala720Ser	missense	Exon 15 of 15	NP_001121900.1	Q8N475-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSTL5	ENST00000306100.10	TSL:1 MANE Select	c.2188G>T	p.Ala730Ser	missense	Exon 16 of 16	ENSP00000305334.4	Q8N475-1
	FSTL5	ENST00000379164.8	TSL:1	c.2185G>T	p.Ala729Ser	missense	Exon 16 of 16	ENSP00000368462.4	Q8N475-2
	FSTL5	ENST00000427802.2	TSL:1	c.2158G>T	p.Ala720Ser	missense	Exon 15 of 15	ENSP00000389270.2	Q8N475-3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00 AC: 0 AN: 250672 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	17
DANN	Uncertain	0.99
DEOGEN2	Benign	0.0026	T
Eigen	Benign	-0.28
Eigen_PC	Benign	-0.14
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Benign	0.80	T
M_CAP	Benign	0.0072	T
MetaRNN	Benign	0.15	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.4	L
PhyloP100		3.9
PrimateAI	Benign	0.40	T
PROVEAN	Benign	-0.69	N
REVEL	Benign	0.044
Sift	Benign	0.47	T
Sift4G	Benign	0.31	T
Polyphen		0.047	B
Vest4		0.23
MutPred		0.45		Loss of sheet (P = 0.1158)
MVP		0.35
MPC		0.32
ClinPred		0.72	D
GERP RS		4.8
Varity_R		0.090
gMVP		0.31
Mutation Taster		=94/6	polymorphism

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: rs764053528; hg19: chr4-162307255;