rs973516

Variant names:

• chr4-162087086-C-T
• rs973516
• NM_020116.5:c.126+24185G>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.126+24185G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 151,884 control chromosomes in the GnomAD database, including 30,407 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 0.63 (30407 hom., cov: 33)
• Consequence: FSTL5 NM_020116.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 4 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSTL5	NM_020116.5	c.126+24185G>A		intron_variant	Intron 2 of 15	ENST00000306100.10	NP_064501.2
FSTL5	NM_001128427.3	c.126+24185G>A		intron_variant	Intron 2 of 15		NP_001121899.1
FSTL5	NM_001128428.3	c.126+24185G>A		intron_variant	Intron 2 of 14		NP_001121900.1
FSTL5	XM_011532126.1	c.126+24185G>A		intron_variant	Intron 2 of 14		XP_011530428.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FSTL5	ENST00000306100.10	c.126+24185G>A		intron_variant	Intron 2 of 15	1	NM_020116.5	ENSP00000305334.4
FSTL5	ENST00000379164.8	c.126+24185G>A		intron_variant	Intron 2 of 15	1		ENSP00000368462.4
FSTL5	ENST00000427802.2	c.126+24185G>A		intron_variant	Intron 2 of 14	1		ENSP00000389270.2

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95667 AN: 151766 Hom.: 30386 Cov.: 33

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.630 AC: 95738 AN: 151884 Hom.: 30407 Cov.: 33 AF XY: 0.627 AC XY: 46500 AN XY: 74214

African (AFR) AF: 0.619 AC: 25664 AN: 41466

American (AMR) AF: 0.703 AC: 10710 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2579 AN: 3470

East Asian (EAS) AF: 0.549 AC: 2828 AN: 5152

South Asian (SAS) AF: 0.645 AC: 3103 AN: 4814

European-Finnish (FIN) AF: 0.522 AC: 5502 AN: 10534

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43007 AN: 67896

Other (OTH) AF: 0.666 AC: 1410 AN: 2116

Alfa AF: 0.644 Hom.: 97716

Bravo AF: 0.644

Asia WGS AF: 0.635 AC: 2194 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.55
DANN	Benign	0.38
PhyloP100		-2.1
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: rs973516; hg19: chr4-163008238;