rs4560355

Variant names:

• chr4-161639230-A-T
• rs4560355
• NM_020116.5:c.894+17098T>A

Variant summary

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

The NM_020116.5(FSTL5):​c.894+17098T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0759 in 152,062 control chromosomes in the GnomAD database, including 1,235 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 0.076 (1235 hom., cov: 31)
• Consequence: FSTL5 NM_020116.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102
• 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]

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 = 0.238 is higher than 0.05.

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.894+17098T>A		intron	N/A	NP_064501.2	Q8N475-1
	FSTL5	NM_001128427.3		c.891+17098T>A		intron	N/A	NP_001121899.1	Q8N475-2
	FSTL5	NM_001128428.3		c.891+17098T>A		intron	N/A	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.894+17098T>A		intron	N/A	ENSP00000305334.4	Q8N475-1
	FSTL5	ENST00000379164.8	TSL:1	c.891+17098T>A		intron	N/A	ENSP00000368462.4	Q8N475-2
	FSTL5	ENST00000427802.2	TSL:1	c.891+17098T>A		intron	N/A	ENSP00000389270.2	Q8N475-3

Frequencies

GnomAD3 genomes AF: 0.0759 AC: 11526 AN: 151944 Hom.: 1229 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0322

Gnomad ASJ AF: 0.00433

Gnomad EAS AF: 0.0359

Gnomad SAS AF: 0.0474

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00697

Gnomad OTH AF: 0.0583

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

GnomAD4 genome AF: 0.0759 AC: 11543 AN: 152062 Hom.: 1235 Cov.: 31 AF XY: 0.0733 AC XY: 5446 AN XY: 74348

African (AFR) AF: 0.242 AC: 10004 AN: 41422

American (AMR) AF: 0.0322 AC: 492 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.00433 AC: 15 AN: 3462

East Asian (EAS) AF: 0.0357 AC: 184 AN: 5148

South Asian (SAS) AF: 0.0473 AC: 228 AN: 4824

European-Finnish (FIN) AF: 0.000283 AC: 3 AN: 10598

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.00694 AC: 472 AN: 68014

Other (OTH) AF: 0.0577 AC: 122 AN: 2114

Alfa AF: 0.0473 Hom.: 82

Bravo AF: 0.0849

Asia WGS AF: 0.0550 AC: 191 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.34
PhyloP100		0.10
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: rs4560355; hg19: chr4-162560382;