4-161690750-T-C

Variant names:

• chr4-161690750-T-C
• rs10857341
• NM_020116.5:c.728-34256A>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.728-34256A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.878 in 152,078 control chromosomes in the GnomAD database, including 59,228 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 0.88 (59228 hom., cov: 31)
• Consequence: FSTL5 NM_020116.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSTL5	NM_020116.5	c.728-34256A>G		intron_variant	Intron 6 of 15	ENST00000306100.10	NP_064501.2
FSTL5	NM_001128427.3	c.725-34256A>G		intron_variant	Intron 6 of 15		NP_001121899.1
FSTL5	NM_001128428.3	c.725-34256A>G		intron_variant	Intron 6 of 14		NP_001121900.1
FSTL5	XM_011532126.1	c.728-34256A>G		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.728-34256A>G		intron_variant	Intron 6 of 15	1	NM_020116.5	ENSP00000305334.4
FSTL5	ENST00000379164.8	c.725-34256A>G		intron_variant	Intron 6 of 15	1		ENSP00000368462.4
FSTL5	ENST00000427802.2	c.725-34256A>G		intron_variant	Intron 6 of 14	1		ENSP00000389270.2

Frequencies

GnomAD3 genomes AF: 0.878 AC: 133494 AN: 151960 Hom.: 59207 Cov.: 31

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.954

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.944

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.878 AC: 133563 AN: 152078 Hom.: 59228 Cov.: 31 AF XY: 0.875 AC XY: 65013 AN XY: 74330

African (AFR) AF: 0.752 AC: 31194 AN: 41470

American (AMR) AF: 0.903 AC: 13797 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.934 AC: 3234 AN: 3462

East Asian (EAS) AF: 0.815 AC: 4199 AN: 5150

South Asian (SAS) AF: 0.802 AC: 3863 AN: 4816

European-Finnish (FIN) AF: 0.954 AC: 10117 AN: 10602

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.944 AC: 64158 AN: 67978

Other (OTH) AF: 0.880 AC: 1859 AN: 2112

Alfa AF: 0.907 Hom.: 9425

Bravo AF: 0.873

Asia WGS AF: 0.801 AC: 2788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.60
PhyloP100		-1.4
Mutation Taster		=22/78	disease causing

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: rs10857341; hg19: chr4-162611902;