chr4-161859843-G-A

Variant names:

• chr4-161859843-G-A
• rs10517754
• NM_020116.5:c.409+60561C>T

Variant summary

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

The NM_020116.5(FSTL5):​c.409+60561C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0849 in 152,150 control chromosomes in the GnomAD database, including 645 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 0.085 (645 hom., cov: 32)
• Consequence: FSTL5 NM_020116.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.795
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSTL5	NM_020116.5	c.409+60561C>T		intron_variant	Intron 4 of 15	ENST00000306100.10	NP_064501.2
FSTL5	NM_001128427.3	c.406+60561C>T		intron_variant	Intron 4 of 15		NP_001121899.1
FSTL5	NM_001128428.3	c.406+60561C>T		intron_variant	Intron 4 of 14		NP_001121900.1
FSTL5	XM_011532126.1	c.409+60561C>T		intron_variant	Intron 4 of 14		XP_011530428.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FSTL5	ENST00000306100.10	c.409+60561C>T		intron_variant	Intron 4 of 15	1	NM_020116.5	ENSP00000305334.4
FSTL5	ENST00000379164.8	c.406+60561C>T		intron_variant	Intron 4 of 15	1		ENSP00000368462.4
FSTL5	ENST00000427802.2	c.406+60561C>T		intron_variant	Intron 4 of 14	1		ENSP00000389270.2

Frequencies

GnomAD3 genomes AF: 0.0849 AC: 12914 AN: 152030 Hom.: 644 Cov.: 32

Gnomad AFR AF: 0.0520

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0897

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0927

Gnomad OTH AF: 0.0673

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

GnomAD4 genome AF: 0.0849 AC: 12916 AN: 152150 Hom.: 645 Cov.: 32 AF XY: 0.0864 AC XY: 6425 AN XY: 74366

African (AFR) AF: 0.0519 AC: 2155 AN: 41518

American (AMR) AF: 0.0894 AC: 1365 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3470

East Asian (EAS) AF: 0.155 AC: 799 AN: 5160

South Asian (SAS) AF: 0.129 AC: 625 AN: 4830

European-Finnish (FIN) AF: 0.116 AC: 1227 AN: 10570

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0927 AC: 6304 AN: 68004

Other (OTH) AF: 0.0666 AC: 141 AN: 2116

Alfa AF: 0.0774 Hom.: 288

Bravo AF: 0.0790

Asia WGS AF: 0.121 AC: 420 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	3.8
DANN	Benign	0.65
PhyloP100		0.80
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: rs10517754; hg19: chr4-162780995;