rs10521868

Positions:

• chrX-147909986-C-A

Variant summary

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

The NR_024503.3(FMR1-AS1):​n.1186G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0907 in 112,182 control chromosomes in the GnomAD database, including 392 homozygotes. There are 2,913 hemizygotes in GnomAD. 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 0.091 (392 hom., 2913 hem., cov: 24)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: FMR1-AS1 NR_024503.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520

Genes affected

FMR1-AS1 (HGNC:39081): (FMR1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FMR1-AS1	NR_024503.3	n.1186G>T		non_coding_transcript_exon_variant	2/2
FMR1-AS1	NR_024499.3	n.1832G>T		non_coding_transcript_exon_variant	1/1
FMR1-AS1	NR_024501.3	n.1450G>T		non_coding_transcript_exon_variant	2/2
FMR1-AS1	NR_024502.3	n.1290G>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FMR1-AS1	ENST00000594922.5	n.1450G>T		non_coding_transcript_exon_variant	2/2	1
FMR1-AS1	ENST00000596112.5	n.1290G>T		non_coding_transcript_exon_variant	3/3	1
FMR1-AS1	ENST00000598667.1	n.1186G>T		non_coding_transcript_exon_variant	2/2	1
FMR1-AS1	ENST00000601841.1	n.1832G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0907 AC: 10174 AN: 112131 Hom.: 393 Cov.: 24 AF XY: 0.0847 AC XY: 2907 AN XY: 34301

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.0585

Gnomad ASJ AF: 0.0612

Gnomad EAS AF: 0.000829

Gnomad SAS AF: 0.0252

Gnomad FIN AF: 0.0911

Gnomad MID AF: 0.100

Gnomad NFE AF: 0.0847

Gnomad OTH AF: 0.0810

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 5 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 3

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0907 AC: 10179 AN: 112182 Hom.: 392 Cov.: 24 AF XY: 0.0848 AC XY: 2913 AN XY: 34362

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0585

Gnomad4 ASJ AF: 0.0612

Gnomad4 EAS AF: 0.000831

Gnomad4 SAS AF: 0.0253

Gnomad4 FIN AF: 0.0911

Gnomad4 NFE AF: 0.0847

Gnomad4 OTH AF: 0.0801

Alfa AF: 0.0824 Hom.: 3108

Bravo AF: 0.0922

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.10
DANN	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10521868; hg19: chrX-146991504;