4-161929201-C-T

Variant names:

• chr4-161929201-C-T
• rs359491
• NM_020116.5:c.161-8549G>A

Variant summary

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

The NM_020116.5(FSTL5):​c.161-8549G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0629 in 149,410 control chromosomes in the GnomAD database, including 807 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 0.063 (807 hom., cov: 31)
• Consequence: FSTL5 NM_020116.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSTL5	NM_020116.5	c.161-8549G>A		intron_variant	Intron 3 of 15	ENST00000306100.10	NP_064501.2
FSTL5	NM_001128427.3	c.158-8549G>A		intron_variant	Intron 3 of 15		NP_001121899.1
FSTL5	NM_001128428.3	c.158-8549G>A		intron_variant	Intron 3 of 14		NP_001121900.1
FSTL5	XM_011532126.1	c.161-8549G>A		intron_variant	Intron 3 of 14		XP_011530428.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FSTL5	ENST00000306100.10	c.161-8549G>A		intron_variant	Intron 3 of 15	1	NM_020116.5	ENSP00000305334.4
FSTL5	ENST00000379164.8	c.158-8549G>A		intron_variant	Intron 3 of 15	1		ENSP00000368462.4
FSTL5	ENST00000427802.2	c.158-8549G>A		intron_variant	Intron 3 of 14	1		ENSP00000389270.2

Frequencies

GnomAD3 genomes AF: 0.0628 AC: 9373 AN: 149366 Hom.: 803 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0344

Gnomad ASJ AF: 0.00725

Gnomad EAS AF: 0.0379

Gnomad SAS AF: 0.0807

Gnomad FIN AF: 0.000202

Gnomad MID AF: 0.0325

Gnomad NFE AF: 0.00436

Gnomad OTH AF: 0.0585

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

GnomAD4 genome AF: 0.0629 AC: 9393 AN: 149410 Hom.: 807 Cov.: 31 AF XY: 0.0616 AC XY: 4484 AN XY: 72808

African (AFR) AF: 0.193 AC: 7855 AN: 40664

American (AMR) AF: 0.0344 AC: 513 AN: 14926

Ashkenazi Jewish (ASJ) AF: 0.00725 AC: 25 AN: 3448

East Asian (EAS) AF: 0.0384 AC: 195 AN: 5080

South Asian (SAS) AF: 0.0802 AC: 380 AN: 4740

European-Finnish (FIN) AF: 0.000202 AC: 2 AN: 9892

Middle Eastern (MID) AF: 0.0319 AC: 9 AN: 282

European-Non Finnish (NFE) AF: 0.00436 AC: 294 AN: 67404

Other (OTH) AF: 0.0581 AC: 120 AN: 2064

Alfa AF: 0.00215 Hom.: 2

Bravo AF: 0.0689

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.4
DANN	Benign	0.18
PhyloP100		1.3
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: rs359491; hg19: chr4-162850353;