chr4-161464090-A-C

Variant names:

• chr4-161464090-A-C
• rs10517745
• NM_020116.5:c.1609-4771T>G

Variant summary

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

The NM_020116.5(FSTL5):​c.1609-4771T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0539 in 152,206 control chromosomes in the GnomAD database, including 612 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 0.054 (612 hom., cov: 32)
• Consequence: FSTL5 NM_020116.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.521
• Publications: 0 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSTL5	NM_020116.5	c.1609-4771T>G		intron_variant	Intron 13 of 15	ENST00000306100.10	NP_064501.2
FSTL5	NM_001128427.3	c.1606-4771T>G		intron_variant	Intron 13 of 15		NP_001121899.1
FSTL5	NM_001128428.3	c.1579-4771T>G		intron_variant	Intron 12 of 14		NP_001121900.1
FSTL5	XM_011532126.1	c.1582-4771T>G		intron_variant	Intron 12 of 14		XP_011530428.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FSTL5	ENST00000306100.10	c.1609-4771T>G		intron_variant	Intron 13 of 15	1	NM_020116.5	ENSP00000305334.4
FSTL5	ENST00000379164.8	c.1606-4771T>G		intron_variant	Intron 13 of 15	1		ENSP00000368462.4
FSTL5	ENST00000427802.2	c.1579-4771T>G		intron_variant	Intron 12 of 14	1		ENSP00000389270.2

Frequencies

GnomAD3 genomes AF: 0.0538 AC: 8175 AN: 152088 Hom.: 610 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0230

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0465

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00558

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0539 AC: 8206 AN: 152206 Hom.: 612 Cov.: 32 AF XY: 0.0529 AC XY: 3938 AN XY: 74428

African (AFR) AF: 0.172 AC: 7129 AN: 41486

American (AMR) AF: 0.0229 AC: 350 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00259 AC: 9 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5178

South Asian (SAS) AF: 0.0464 AC: 224 AN: 4830

European-Finnish (FIN) AF: 0.000377 AC: 4 AN: 10606

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00559 AC: 380 AN: 68036

Other (OTH) AF: 0.0431 AC: 91 AN: 2112

Alfa AF: 0.0324 Hom.: 100

Bravo AF: 0.0594

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.66
PhyloP100		0.52
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: rs10517745; hg19: chr4-162385242;