rs11653545

Variant names:

• chr17-7608756-G-A
• rs11653545
• NM_004860.4:c.82-2607C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-7608756-G-A
• chr17-7608756-G-C

Variant summary

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

The NM_004860.4(FXR2):​c.82-2607C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0285 in 152,272 control chromosomes in the GnomAD database, including 226 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 0.028 (226 hom., cov: 32)
• Consequence: FXR2 NM_004860.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455

Genes affected

FXR2 (HGNC:4024): (FMR1 autosomal homolog 2) The protein encoded by this gene is a RNA binding protein containing two KH domains and one RCG box, which is similar to FMRP and FXR1. It associates with polyribosomes, predominantly with 60S large ribosomal subunits. This encoded protein may self-associate or interact with FMRP and FXR1. It may have a role in the development of fragile X cognitive disability syndrome. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FXR2	NM_004860.4	c.82-2607C>T		intron_variant	Intron 1 of 16	ENST00000250113.12	NP_004851.2
FXR2	XM_047437106.1	c.82-2607C>T		intron_variant	Intron 1 of 16		XP_047293062.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FXR2	ENST00000250113.12	c.82-2607C>T		intron_variant	Intron 1 of 16	1	NM_004860.4	ENSP00000250113.7
FXR2	ENST00000704984.1	c.301-2607C>T		intron_variant	Intron 1 of 16			ENSP00000516064.1
FXR2	ENST00000571597.1	c.-129-2607C>T		intron_variant	Intron 1 of 5	4		ENSP00000459230.1

Frequencies

GnomAD3 genomes AF: 0.0284 AC: 4323 AN: 152154 Hom.: 224 Cov.: 32

Gnomad AFR AF: 0.00881

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.0273

Gnomad FIN AF: 0.00255

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0170

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0285 AC: 4337 AN: 152272 Hom.: 226 Cov.: 32 AF XY: 0.0311 AC XY: 2313 AN XY: 74440

Gnomad4 AFR AF: 0.00879

Gnomad4 AMR AF: 0.0818

Gnomad4 ASJ AF: 0.0317

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.0279

Gnomad4 FIN AF: 0.00255

Gnomad4 NFE AF: 0.0171

Gnomad4 OTH AF: 0.0326

Alfa AF: 0.0240 Hom.: 198

Bravo AF: 0.0358

Asia WGS AF: 0.0970 AC: 339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
DANN	Benign	0.65

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: rs11653545; hg19: chr17-7512074;