ENST00000594922.5:n.1450G>T

Variant names:

• chrX-147909986-C-A
• rs10521868
• ENST00000594922.5:n.1450G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000594922.5(FMR1-AS1):​n.1450G>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 ENST00000594922.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FMR1-AS1	NR_024499.3	n.1832G>T		non_coding_transcript_exon_variant	Exon 1 of 1
FMR1-AS1	NR_024501.3	n.1450G>T		non_coding_transcript_exon_variant	Exon 2 of 2
FMR1-AS1	NR_024502.3	n.1290G>T		non_coding_transcript_exon_variant	Exon 3 of 3
FMR1-AS1	NR_024503.3	n.1186G>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FMR1-AS1	ENST00000594922.5	n.1450G>T		non_coding_transcript_exon_variant	Exon 2 of 2	1
FMR1-AS1	ENST00000596112.5	n.1290G>T		non_coding_transcript_exon_variant	Exon 3 of 3	1
FMR1-AS1	ENST00000598667.1	n.1186G>T		non_coding_transcript_exon_variant	Exon 2 of 2	1

Frequencies

GnomAD3 genomes AF: 0.0907 AC: 10174 AN: 112131 Hom.: 393 Cov.: 24

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AF: 0.00 AC: 0 AN: 1

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

African (AFR) AF: 0.130 AC: 4008 AN: 30789

American (AMR) AF: 0.0585 AC: 626 AN: 10705

Ashkenazi Jewish (ASJ) AF: 0.0612 AC: 162 AN: 2645

East Asian (EAS) AF: 0.000831 AC: 3 AN: 3610

South Asian (SAS) AF: 0.0253 AC: 69 AN: 2726

European-Finnish (FIN) AF: 0.0911 AC: 551 AN: 6046

Middle Eastern (MID) AF: 0.0826 AC: 18 AN: 218

European-Non Finnish (NFE) AF: 0.0847 AC: 4510 AN: 53232

Other (OTH) AF: 0.0801 AC: 123 AN: 1536

Alfa AF: 0.0840 Hom.: 4839

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
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs10521868; hg19: chrX-146991504;