X-147961254-C-T

Variant summary

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

The variant allele was found at a frequency of 0.133 in 111,310 control chromosomes in the GnomAD database, including 1,314 homozygotes. There are 4,091 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 0.13 ( 1314 hom., 4091 hem., cov: 23)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.331
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.133
AC:
14820
AN:
111258
Hom.:
1316
Cov.:
23
AF XY:
0.122
AC XY:
4080
AN XY:
33496
show subpopulations
Gnomad AFR
AF:
0.325
Gnomad AMI
AF:
0.0176
Gnomad AMR
AF:
0.0602
Gnomad ASJ
AF:
0.0423
Gnomad EAS
AF:
0.00198
Gnomad SAS
AF:
0.115
Gnomad FIN
AF:
0.0248
Gnomad MID
AF:
0.119
Gnomad NFE
AF:
0.0664
Gnomad OTH
AF:
0.124
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.133
AC:
14826
AN:
111310
Hom.:
1314
Cov.:
23
AF XY:
0.122
AC XY:
4091
AN XY:
33558
show subpopulations
Gnomad4 AFR
AF:
0.325
Gnomad4 AMR
AF:
0.0601
Gnomad4 ASJ
AF:
0.0423
Gnomad4 EAS
AF:
0.00198
Gnomad4 SAS
AF:
0.114
Gnomad4 FIN
AF:
0.0248
Gnomad4 NFE
AF:
0.0664
Gnomad4 OTH
AF:
0.124
Alfa
AF:
0.0805
Hom.:
2363
Bravo
AF:
0.146

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.65
DANN
Benign
0.81

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: rs5904818; hg19: chrX-147042774; API