rs10517743

Positions:

• chr4-161386982-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020116.5(FSTL5):​c.1842-533C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0399 in 153,954 control chromosomes in the GnomAD database, including 326 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 0.040 (320 hom., cov: 33)
  • Exomes 𝑓: 0.057 (6 hom.)
• Consequence: FSTL5 NM_020116.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FSTL5	NM_020116.5	c.1842-533C>G		intron_variant		ENST00000306100.10
FSTL5	NM_001128427.3	c.1839-533C>G		intron_variant
FSTL5	NM_001128428.3	c.1812-533C>G		intron_variant
FSTL5	XM_011532126.1	c.1815-533C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FSTL5	ENST00000306100.10	c.1842-533C>G		intron_variant		1	NM_020116.5	P5
FSTL5	ENST00000379164.8	c.1839-533C>G		intron_variant		1		A1
FSTL5	ENST00000427802.2	c.1812-533C>G		intron_variant		1		A1
	ENST00000508189.1	n.1405G>C		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.0395 AC: 5998 AN: 151758 Hom.: 312 Cov.: 33

Gnomad AFR AF: 0.00542

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.0370

Gnomad MID AF: 0.0128

Gnomad NFE AF: 0.0251

Gnomad OTH AF: 0.0458

GnomAD4 exome AF: 0.0568 AC: 118 AN: 2078 Hom.: 6 Cov.: 0 AF XY: 0.0578 AC XY: 63 AN XY: 1090

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.148

Gnomad4 EAS exome AF: 0.143

Gnomad4 SAS exome AF: 0.137

Gnomad4 NFE exome AF: 0.0188

Gnomad4 OTH exome AF: 0.0313

GnomAD4 genome AF: 0.0397 AC: 6026 AN: 151876 Hom.: 320 Cov.: 33 AF XY: 0.0444 AC XY: 3293 AN XY: 74238

Gnomad4 AFR AF: 0.00540

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.0370

Gnomad4 NFE AF: 0.0251

Gnomad4 OTH AF: 0.0534

Alfa AF: 0.0388 Hom.: 25

Bravo AF: 0.0414

Asia WGS AF: 0.193 AC: 663 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.37
DANN	Benign	0.57

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: rs10517743; hg19: chr4-162308134;