rs1009948

Variant summary

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

The ENST00000429829.6(XIST):​n.11407-464G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0932 in 112,963 control chromosomes in the GnomAD database, including 615 homozygotes. There are 2,871 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 0.094 ( 611 hom., 2839 hem., cov: 22)
Exomes 𝑓: 0.068 ( 4 hom. 32 hem. )

Consequence

XIST
ENST00000429829.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.11
Variant links:
Genes affected

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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
XISTNR_001564.2 linkuse as main transcriptn.11437-464G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
XISTENST00000429829.6 linkuse as main transcriptn.11407-464G>A intron_variant 1
XISTENST00000421322.3 linkuse as main transcriptn.579-464G>A intron_variant 2
XISTENST00000434839.3 linkuse as main transcriptn.165-464G>A intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.0936
AC:
10390
AN:
110985
Hom.:
611
Cov.:
22
AF XY:
0.0853
AC XY:
2834
AN XY:
33223
show subpopulations
Gnomad AFR
AF:
0.208
Gnomad AMI
AF:
0.0117
Gnomad AMR
AF:
0.0571
Gnomad ASJ
AF:
0.117
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0504
Gnomad FIN
AF:
0.0126
Gnomad MID
AF:
0.0798
Gnomad NFE
AF:
0.0528
Gnomad OTH
AF:
0.0860
GnomAD4 exome
AF:
0.0681
AC:
131
AN:
1925
Hom.:
4
AF XY:
0.256
AC XY:
32
AN XY:
125
show subpopulations
Gnomad4 AFR exome
AF:
0.333
Gnomad4 AMR exome
AF:
0.0724
Gnomad4 ASJ exome
AF:
0.227
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0247
Gnomad4 FIN exome
AF:
0.0227
Gnomad4 NFE exome
AF:
0.0677
Gnomad4 OTH exome
AF:
0.0833
GnomAD4 genome
AF:
0.0936
AC:
10393
AN:
111038
Hom.:
611
Cov.:
22
AF XY:
0.0853
AC XY:
2839
AN XY:
33286
show subpopulations
Gnomad4 AFR
AF:
0.208
Gnomad4 AMR
AF:
0.0569
Gnomad4 ASJ
AF:
0.117
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0506
Gnomad4 FIN
AF:
0.0126
Gnomad4 NFE
AF:
0.0528
Gnomad4 OTH
AF:
0.0850
Alfa
AF:
0.0601
Hom.:
2230
Bravo
AF:
0.103

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.18
DANN
Benign
0.074

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.

Other links and lift over

dbSNP: rs1009948; hg19: chrX-73053673; API