rs1010471

chr3-180973304-G-A

Variant summary

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

The NM_005087.4(FXR1):c.1604-2009G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,016 control chromosomes in the GnomAD database, including 21,461 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 0.50 (21461 hom., cov: 33)
• Consequence: FXR1 NM_005087.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.02

Genes affected

FXR1 (HGNC:4023): (FMR1 autosomal homolog 1) The protein encoded by this gene is an RNA binding protein that interacts with the functionally-similar proteins FMR1 and FXR2. These proteins shuttle between the nucleus and cytoplasm and associate with polyribosomes, predominantly with the 60S ribosomal subunit. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FXR1	NM_005087.4	c.1604-2009G>A		intron_variant		ENST00000357559.9
FXR1	NM_001013438.3	c.1604-2818G>A		intron_variant
FXR1	NM_001013439.3	c.1349-2009G>A		intron_variant
FXR1	NM_001363882.1	c.1349-2818G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FXR1	ENST00000357559.9	c.1604-2009G>A		intron_variant		1	NM_005087.4

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75410 AN: 151900 Hom.: 21400 Cov.: 33

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.497 AC: 75531 AN: 152016 Hom.: 21461 Cov.: 33 AF XY: 0.492 AC XY: 36591 AN XY: 74302

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.499

Alfa AF: 0.405 Hom.: 6012

Bravo AF: 0.516

Asia WGS AF: 0.577 AC: 2003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.0060
Dann	Benign	0.61

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: rs1010471; hg19: chr3-180691092;