4-161929201-C-T

Position:

• chr4-161929201-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
FSTL5	NM_020116.5	c.161-8549G>A		intron_variant		ENST00000306100.10
FSTL5	NM_001128427.3	c.158-8549G>A		intron_variant
FSTL5	NM_001128428.3	c.158-8549G>A		intron_variant
FSTL5	XM_011532126.1	c.161-8549G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FSTL5	ENST00000306100.10	c.161-8549G>A		intron_variant		1	NM_020116.5	P5
FSTL5	ENST00000379164.8	c.158-8549G>A		intron_variant		1		A1
FSTL5	ENST00000427802.2	c.158-8549G>A		intron_variant		1		A1

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

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.0344

Gnomad4 ASJ AF: 0.00725

Gnomad4 EAS AF: 0.0384

Gnomad4 SAS AF: 0.0802

Gnomad4 FIN AF: 0.000202

Gnomad4 NFE AF: 0.00436

Gnomad4 OTH AF: 0.0581

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs359491; hg19: chr4-162850353;