rs9998941

Variant names:

• chr4-161403710-G-A
• rs9998941
• NM_020116.5:c.1842-17261C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-161403710-G-A
• chr4-161403710-G-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.1842-17261C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,078 control chromosomes in the GnomAD database, including 5,922 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 0.27 (5922 hom., cov: 32)
• Consequence: FSTL5 NM_020116.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020116.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSTL5	NM_020116.5	MANE Select	c.1842-17261C>T		intron	N/A	NP_064501.2	Q8N475-1
	FSTL5	NM_001128427.3		c.1839-17261C>T		intron	N/A	NP_001121899.1	Q8N475-2
	FSTL5	NM_001128428.3		c.1812-17261C>T		intron	N/A	NP_001121900.1	Q8N475-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSTL5	ENST00000306100.10	TSL:1 MANE Select	c.1842-17261C>T		intron	N/A	ENSP00000305334.4	Q8N475-1
	FSTL5	ENST00000379164.8	TSL:1	c.1839-17261C>T		intron	N/A	ENSP00000368462.4	Q8N475-2
	FSTL5	ENST00000427802.2	TSL:1	c.1812-17261C>T		intron	N/A	ENSP00000389270.2	Q8N475-3

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41701 AN: 151960 Hom.: 5925 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.274 AC: 41723 AN: 152078 Hom.: 5922 Cov.: 32 AF XY: 0.276 AC XY: 20531 AN XY: 74320

African (AFR) AF: 0.255 AC: 10601 AN: 41496

American (AMR) AF: 0.291 AC: 4439 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1328 AN: 3468

East Asian (EAS) AF: 0.462 AC: 2383 AN: 5162

South Asian (SAS) AF: 0.386 AC: 1861 AN: 4820

European-Finnish (FIN) AF: 0.230 AC: 2430 AN: 10568

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17878 AN: 67980

Other (OTH) AF: 0.267 AC: 565 AN: 2114

Alfa AF: 0.269 Hom.: 3346

Bravo AF: 0.277

Asia WGS AF: 0.333 AC: 1155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.27
PhyloP100		0.043
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: rs9998941; hg19: chr4-162324862;