rs17638464

Variant names:

• chr4-161681057-G-A
• rs17638464
• NM_020116.5:c.728-24563C>T

Variant summary

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

The NM_020116.5(FSTL5):​c.728-24563C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.068 in 152,112 control chromosomes in the GnomAD database, including 425 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 0.068 (425 hom., cov: 32)
• Consequence: FSTL5 NM_020116.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSTL5	NM_020116.5	c.728-24563C>T		intron_variant	Intron 6 of 15	ENST00000306100.10	NP_064501.2
FSTL5	NM_001128427.3	c.725-24563C>T		intron_variant	Intron 6 of 15		NP_001121899.1
FSTL5	NM_001128428.3	c.725-24563C>T		intron_variant	Intron 6 of 14		NP_001121900.1
FSTL5	XM_011532126.1	c.728-24563C>T		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.728-24563C>T		intron_variant	Intron 6 of 15	1	NM_020116.5	ENSP00000305334.4
FSTL5	ENST00000379164.8	c.725-24563C>T		intron_variant	Intron 6 of 15	1		ENSP00000368462.4
FSTL5	ENST00000427802.2	c.725-24563C>T		intron_variant	Intron 6 of 14	1		ENSP00000389270.2

Frequencies

GnomAD3 genomes AF: 0.0679 AC: 10315 AN: 151994 Hom.: 420 Cov.: 32

Gnomad AFR AF: 0.0765

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0713

Gnomad ASJ AF: 0.0602

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0448

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0502

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0680 AC: 10343 AN: 152112 Hom.: 425 Cov.: 32 AF XY: 0.0725 AC XY: 5392 AN XY: 74358

Gnomad4 AFR AF: 0.0765

Gnomad4 AMR AF: 0.0716

Gnomad4 ASJ AF: 0.0602

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.0448

Gnomad4 NFE AF: 0.0501

Gnomad4 OTH AF: 0.0766

Alfa AF: 0.0586 Hom.: 651

Bravo AF: 0.0653

Asia WGS AF: 0.172 AC: 596 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.72

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: rs17638464; hg19: chr4-162602209;