Variant X-147909986-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.520

Variant links:

Genes affected

FMR1-AS1 (HGNC:):

FMR1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Effect	#exon/exons
FMR1-AS1	NR_024499.3 linkuse as main transcript	n.1832G>T	non_coding_transcript_exon_variant	1/1
FMR1-AS1	NR_024501.3 linkuse as main transcript	n.1450G>T	non_coding_transcript_exon_variant	2/2
FMR1-AS1	NR_024502.3 linkuse as main transcript	n.1290G>T	non_coding_transcript_exon_variant	3/3
FMR1-AS1	NR_024503.3 linkuse as main transcript	n.1186G>T	non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
FMR1-AS1	ENST00000594922.5 linkuse as main transcript	n.1450G>T	non_coding_transcript_exon_variant	2/2	1
FMR1-AS1	ENST00000596112.5 linkuse as main transcript	n.1290G>T	non_coding_transcript_exon_variant	3/3	1
FMR1-AS1	ENST00000598667.1 linkuse as main transcript	n.1186G>T	non_coding_transcript_exon_variant	2/2	1
FMR1-AS1	ENST00000601841.1 linkuse as main transcript	n.1832G>T	non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes

AF:

0.0907

AC:

10174

AN:

112131

Hom.:

393

Cov.:

AF XY:

0.0847

AC XY:

2907

AN XY:

34301

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0907

AC:

10179

AN:

112182

Hom.:

392

Cov.:

AF XY:

0.0848

AC XY:

2913

AN XY:

34362

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over