rs2149592

chr9-105467709-A-G

Variant summary

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

The NM_001145313.3(FSD1L):c.208-484A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,174 control chromosomes in the GnomAD database, including 1,687 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 0.12 (1687 hom., cov: 32)
• Consequence: FSD1L NM_001145313.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.906

Genes affected

FSD1L (HGNC:13753): (fibronectin type III and SPRY domain containing 1 like) Predicted to be located in cytoplasm. Predicted to be integral component of membrane. [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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FSD1L	NM_001145313.3	c.208-484A>G		intron_variant		ENST00000481272.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FSD1L	ENST00000481272.6	c.208-484A>G		intron_variant		2	NM_001145313.3

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18370 AN: 152056 Hom.: 1683 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.0883

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0725

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0631

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.121 AC: 18393 AN: 152174 Hom.: 1687 Cov.: 32 AF XY: 0.119 AC XY: 8850 AN XY: 74394

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.0882

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0725

Gnomad4 NFE AF: 0.0632

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0966 Hom.: 204

Bravo AF: 0.127

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	11
Dann	Benign	0.71

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: rs2149592; hg19: chr9-108229990;