chr4-161911701-A-T

Position:

• chr4-161911701-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020116.5(FSTL5):​c.409+8703T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,114 control chromosomes in the GnomAD database, including 52,040 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 (52040 hom., cov: 33)
• Consequence: FSTL5 NM_020116.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FSTL5	NM_020116.5	c.409+8703T>A		intron_variant		ENST00000306100.10
FSTL5	NM_001128427.3	c.406+8703T>A		intron_variant
FSTL5	NM_001128428.3	c.406+8703T>A		intron_variant
FSTL5	XM_011532126.1	c.409+8703T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FSTL5	ENST00000306100.10	c.409+8703T>A		intron_variant		1	NM_020116.5	P5
FSTL5	ENST00000379164.8	c.406+8703T>A		intron_variant		1		A1
FSTL5	ENST00000427802.2	c.406+8703T>A		intron_variant		1		A1

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124749 AN: 151996 Hom.: 52013 Cov.: 33

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.855

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.821 AC: 124824 AN: 152114 Hom.: 52040 Cov.: 33 AF XY: 0.822 AC XY: 61123 AN XY: 74352

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.855

Gnomad4 ASJ AF: 0.933

Gnomad4 EAS AF: 0.814

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.899

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.837

Alfa AF: 0.831 Hom.: 3147

Bravo AF: 0.810

Asia WGS AF: 0.808 AC: 2809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.50

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: rs6536628; hg19: chr4-162832853;