rs10517752

Variant names:

• chr4-161741954-A-G
• rs10517752
• NM_020116.5:c.727+17457T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020116.5(FSTL5):​c.727+17457T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,968 control chromosomes in the GnomAD database, including 2,346 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 0.16 (2346 hom., cov: 31)
• Consequence: FSTL5 NM_020116.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410
• Publications: 3 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSTL5	NM_020116.5	c.727+17457T>C		intron_variant	Intron 6 of 15	ENST00000306100.10	NP_064501.2
FSTL5	NM_001128427.3	c.724+17457T>C		intron_variant	Intron 6 of 15		NP_001121899.1
FSTL5	NM_001128428.3	c.724+17457T>C		intron_variant	Intron 6 of 14		NP_001121900.1
FSTL5	XM_011532126.1	c.727+17457T>C		intron_variant	Intron 6 of 14		XP_011530428.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FSTL5	ENST00000306100.10	c.727+17457T>C		intron_variant	Intron 6 of 15	1	NM_020116.5	ENSP00000305334.4
FSTL5	ENST00000379164.8	c.724+17457T>C		intron_variant	Intron 6 of 15	1		ENSP00000368462.4
FSTL5	ENST00000427802.2	c.724+17457T>C		intron_variant	Intron 6 of 14	1		ENSP00000389270.2

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24010 AN: 151850 Hom.: 2341 Cov.: 31

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0714

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.158 AC: 24029 AN: 151968 Hom.: 2346 Cov.: 31 AF XY: 0.157 AC XY: 11672 AN XY: 74292

African (AFR) AF: 0.279 AC: 11548 AN: 41364

American (AMR) AF: 0.167 AC: 2557 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3472

East Asian (EAS) AF: 0.108 AC: 556 AN: 5148

South Asian (SAS) AF: 0.134 AC: 646 AN: 4824

European-Finnish (FIN) AF: 0.0714 AC: 756 AN: 10590

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6844 AN: 67990

Other (OTH) AF: 0.158 AC: 333 AN: 2104

Alfa AF: 0.124 Hom.: 2348

Bravo AF: 0.171

Asia WGS AF: 0.129 AC: 449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.64
PhyloP100		-0.041
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: rs10517752; hg19: chr4-162663106;