4-161905625-T-C

Variant names:

• chr4-161905625-T-C
• rs1440606
• NM_020116.5:c.409+14779A>G

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+14779A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.826 in 152,060 control chromosomes in the GnomAD database, including 52,542 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 0.83 (52542 hom., cov: 31)
• Consequence: FSTL5 NM_020116.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 0 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020116.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSTL5	NM_020116.5	MANE Select	c.409+14779A>G		intron	N/A	NP_064501.2
	FSTL5	NM_001128427.3		c.406+14779A>G		intron	N/A	NP_001121899.1
	FSTL5	NM_001128428.3		c.406+14779A>G		intron	N/A	NP_001121900.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSTL5	ENST00000306100.10	TSL:1 MANE Select	c.409+14779A>G		intron	N/A	ENSP00000305334.4
	FSTL5	ENST00000379164.8	TSL:1	c.406+14779A>G		intron	N/A	ENSP00000368462.4
	FSTL5	ENST00000427802.2	TSL:1	c.406+14779A>G		intron	N/A	ENSP00000389270.2

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125551 AN: 151942 Hom.: 52513 Cov.: 31

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.826 AC: 125627 AN: 152060 Hom.: 52542 Cov.: 31 AF XY: 0.827 AC XY: 61496 AN XY: 74324

African (AFR) AF: 0.678 AC: 28090 AN: 41434

American (AMR) AF: 0.857 AC: 13070 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.933 AC: 3240 AN: 3472

East Asian (EAS) AF: 0.814 AC: 4215 AN: 5180

South Asian (SAS) AF: 0.823 AC: 3970 AN: 4822

European-Finnish (FIN) AF: 0.893 AC: 9446 AN: 10582

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.893 AC: 60717 AN: 68004

Other (OTH) AF: 0.842 AC: 1773 AN: 2106

Alfa AF: 0.880 Hom.: 34468

Bravo AF: 0.817

Asia WGS AF: 0.809 AC: 2812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.66
PhyloP100		-1.5
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: rs1440606; hg19: chr4-162826777;