chr4-161911701-A-T

Variant names:

• chr4-161911701-A-T
• rs6536628
• NM_020116.5:c.409+8703T>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.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
• 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=-0.91).
• 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 rank	MANE	Protein	UniProt
FSTL5	NM_020116.5	c.409+8703T>A		intron_variant	Intron 4 of 15	ENST00000306100.10	NP_064501.2
FSTL5	NM_001128427.3	c.406+8703T>A		intron_variant	Intron 4 of 15		NP_001121899.1
FSTL5	NM_001128428.3	c.406+8703T>A		intron_variant	Intron 4 of 14		NP_001121900.1
FSTL5	XM_011532126.1	c.409+8703T>A		intron_variant	Intron 4 of 14		XP_011530428.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FSTL5	ENST00000306100.10	c.409+8703T>A		intron_variant	Intron 4 of 15	1	NM_020116.5	ENSP00000305334.4
FSTL5	ENST00000379164.8	c.406+8703T>A		intron_variant	Intron 4 of 15	1		ENSP00000368462.4
FSTL5	ENST00000427802.2	c.406+8703T>A		intron_variant	Intron 4 of 14	1		ENSP00000389270.2

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

African (AFR) AF: 0.653 AC: 27059 AN: 41448

American (AMR) AF: 0.855 AC: 13061 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.933 AC: 3237 AN: 3470

East Asian (EAS) AF: 0.814 AC: 4218 AN: 5184

South Asian (SAS) AF: 0.824 AC: 3971 AN: 4820

European-Finnish (FIN) AF: 0.899 AC: 9518 AN: 10590

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60888 AN: 68000

Other (OTH) AF: 0.837 AC: 1767 AN: 2112

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
PhyloP100		-0.065
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: rs6536628; hg19: chr4-162832853;