chr9-105512650-A-G

Variant names:

• chr9-105512650-A-G
• rs10820812
• NM_001145313.3:c.896-157A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FSD1L	NM_001145313.3	c.896-157A>G		intron_variant	Intron 9 of 13	ENST00000481272.6	NP_001138785.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FSD1L	ENST00000481272.6	c.896-157A>G		intron_variant	Intron 9 of 13	2	NM_001145313.3	ENSP00000417492.1

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

African (AFR) AF: 0.509 AC: 21104 AN: 41454

American (AMR) AF: 0.630 AC: 9625 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1870 AN: 3472

East Asian (EAS) AF: 0.730 AC: 3777 AN: 5176

South Asian (SAS) AF: 0.442 AC: 2130 AN: 4824

European-Finnish (FIN) AF: 0.582 AC: 6150 AN: 10560

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38645 AN: 67878

Other (OTH) AF: 0.582 AC: 1227 AN: 2108

Alfa AF: 0.566 Hom.: 55837

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
PhyloP100		-0.89
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: rs10820812; hg19: chr9-108274931;