NM_020116.5:c.409+19250A>C

Variant names:

• chr4-161901154-T-G
• rs2033404
• NM_020116.5:c.409+19250A>C

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+19250A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 151,462 control chromosomes in the GnomAD database, including 52,127 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 0.82 (52127 hom., cov: 30)
• Consequence: FSTL5 NM_020116.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSTL5	NM_020116.5	c.409+19250A>C		intron_variant	Intron 4 of 15	ENST00000306100.10	NP_064501.2
FSTL5	NM_001128427.3	c.406+19250A>C		intron_variant	Intron 4 of 15		NP_001121899.1
FSTL5	NM_001128428.3	c.406+19250A>C		intron_variant	Intron 4 of 14		NP_001121900.1
FSTL5	XM_011532126.1	c.409+19250A>C		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+19250A>C		intron_variant	Intron 4 of 15	1	NM_020116.5	ENSP00000305334.4
FSTL5	ENST00000379164.8	c.406+19250A>C		intron_variant	Intron 4 of 15	1		ENSP00000368462.4
FSTL5	ENST00000427802.2	c.406+19250A>C		intron_variant	Intron 4 of 14	1		ENSP00000389270.2

Frequencies

GnomAD3 genomes AF: 0.824 AC: 124771 AN: 151360 Hom.: 52107 Cov.: 30

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.892

Gnomad MID AF: 0.865

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.824 AC: 124830 AN: 151462 Hom.: 52127 Cov.: 30 AF XY: 0.825 AC XY: 61042 AN XY: 73974

African (AFR) AF: 0.671 AC: 27697 AN: 41272

American (AMR) AF: 0.856 AC: 13027 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.933 AC: 3238 AN: 3470

East Asian (EAS) AF: 0.813 AC: 4180 AN: 5144

South Asian (SAS) AF: 0.824 AC: 3932 AN: 4772

European-Finnish (FIN) AF: 0.892 AC: 9279 AN: 10398

Middle Eastern (MID) AF: 0.861 AC: 248 AN: 288

European-Non Finnish (NFE) AF: 0.893 AC: 60611 AN: 67890

Other (OTH) AF: 0.842 AC: 1768 AN: 2100

Alfa AF: 0.877 Hom.: 29768

Bravo AF: 0.815

Asia WGS AF: 0.807 AC: 2804 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.15
DANN	Benign	0.52
PhyloP100		-2.2
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: rs2033404; hg19: chr4-162822306;