chr4-161639230-A-T

Position:

• chr4-161639230-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.894+17098T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0759 in 152,062 control chromosomes in the GnomAD database, including 1,235 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 0.076 (1235 hom., cov: 31)
• Consequence: FSTL5 NM_020116.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102

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 (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSTL5	NM_020116.5	c.894+17098T>A		intron_variant		ENST00000306100.10	NP_064501.2
FSTL5	NM_001128427.3	c.891+17098T>A		intron_variant			NP_001121899.1
FSTL5	NM_001128428.3	c.891+17098T>A		intron_variant			NP_001121900.1
FSTL5	XM_011532126.1	c.894+17098T>A		intron_variant			XP_011530428.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FSTL5	ENST00000306100.10	c.894+17098T>A		intron_variant		1	NM_020116.5	ENSP00000305334	P5
FSTL5	ENST00000379164.8	c.891+17098T>A		intron_variant		1		ENSP00000368462	A1
FSTL5	ENST00000427802.2	c.891+17098T>A		intron_variant		1		ENSP00000389270	A1
FSTL5	ENST00000511170.1	n.256+17098T>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0759 AC: 11526 AN: 151944 Hom.: 1229 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0322

Gnomad ASJ AF: 0.00433

Gnomad EAS AF: 0.0359

Gnomad SAS AF: 0.0474

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00697

Gnomad OTH AF: 0.0583

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

GnomAD4 genome AF: 0.0759 AC: 11543 AN: 152062 Hom.: 1235 Cov.: 31 AF XY: 0.0733 AC XY: 5446 AN XY: 74348

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.0322

Gnomad4 ASJ AF: 0.00433

Gnomad4 EAS AF: 0.0357

Gnomad4 SAS AF: 0.0473

Gnomad4 FIN AF: 0.000283

Gnomad4 NFE AF: 0.00694

Gnomad4 OTH AF: 0.0577

Alfa AF: 0.0473 Hom.: 82

Bravo AF: 0.0849

Asia WGS AF: 0.0550 AC: 191 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.34

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: rs4560355; hg19: chr4-162560382;