rs10820812

chr9-105512650-A-Gchr9-105512650-A-T

Variant summary

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

The NM_001145313.3(FSD1L):c.896-157A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,952 control chromosomes in the GnomAD database, including 24,146 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 0.56 (24146 hom., cov: 32)
• Consequence: FSD1L NM_001145313.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.887

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FSD1L	NM_001145313.3	c.896-157A>G		intron_variant		ENST00000481272.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FSD1L	ENST00000481272.6	c.896-157A>G		intron_variant		2	NM_001145313.3

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85032 AN: 151834 Hom.: 24120 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.560 AC: 85104 AN: 151952 Hom.: 24146 Cov.: 32 AF XY: 0.560 AC XY: 41601 AN XY: 74260

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.582

Alfa AF: 0.551 Hom.: 9357

Bravo AF: 0.567

Asia WGS AF: 0.571 AC: 1982 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.34
Dann	Benign	0.48

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: rs10820812; hg19: chr9-108274931;