rs773300554

Variant names:

• chr9-105539267-A-G
• rs773300554
• NM_001145313.3:c.1383A>G

Your query was ambiguous. Multiple possible variants found:

• chr9-105539267-A-G
• chr9-105539267-A-T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001145313.3(FSD1L):​c.1383A>G​(p.Gln461Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000778 in 1,285,154 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 7.8e-7 (0 hom.)
• Consequence: FSD1L NM_001145313.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 0 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]

FKTN-AS1 (HGNC:55797): (FKTN antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP7: Synonymous conserved (PhyloP=0.146 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145313.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSD1L	NM_001145313.3	MANE Select	c.1383A>G	p.Gln461Gln	synonymous	Exon 13 of 14	NP_001138785.1	Q9BXM9-1
	FSD1L	NM_001330739.2		c.1320A>G	p.Gln440Gln	synonymous	Exon 13 of 14	NP_001317668.1	F8W946
	FSD1L	NM_001287191.2		c.1317A>G	p.Gln439Gln	synonymous	Exon 13 of 14	NP_001274120.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSD1L	ENST00000481272.6	TSL:2 MANE Select	c.1383A>G	p.Gln461Gln	synonymous	Exon 13 of 14	ENSP00000417492.1	Q9BXM9-1
	FSD1L	ENST00000374707.1	TSL:1	c.726A>G	p.Gln242Gln	synonymous	Exon 7 of 8	ENSP00000363839.1	Q8N450
	FSD1L	ENST00000955870.1		c.1416A>G	p.Gln472Gln	synonymous	Exon 14 of 15	ENSP00000625929.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.78e-7 AC: 1 AN: 1285154 Hom.: 0 Cov.: 20 AF XY: 0.00000157 AC XY: 1 AN XY: 638164

African (AFR) AF: 0.00 AC: 0 AN: 27684

American (AMR) AF: 0.00 AC: 0 AN: 25516

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23518

East Asian (EAS) AF: 0.0000289 AC: 1 AN: 34608

South Asian (SAS) AF: 0.00 AC: 0 AN: 70936

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46106

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4992

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 997812

Other (OTH) AF: 0.00 AC: 0 AN: 53982

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.3
DANN	Benign	0.35
PhyloP100		0.15
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs773300554; hg19: chr9-108301548;