X-148299501-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.54 ( 12748 hom., 18234 hem., cov: 23)
Failed GnomAD Quality Control

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0710
Variant links:

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ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.544
AC:
60330
AN:
110955
Hom.:
12741
Cov.:
23
AF XY:
0.549
AC XY:
18225
AN XY:
33211
show subpopulations
Gnomad AFR
AF:
0.269
Gnomad AMI
AF:
0.876
Gnomad AMR
AF:
0.718
Gnomad ASJ
AF:
0.541
Gnomad EAS
AF:
0.872
Gnomad SAS
AF:
0.520
Gnomad FIN
AF:
0.671
Gnomad MID
AF:
0.586
Gnomad NFE
AF:
0.629
Gnomad OTH
AF:
0.553
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.544
AC:
60339
AN:
111009
Hom.:
12748
Cov.:
23
AF XY:
0.548
AC XY:
18234
AN XY:
33275
show subpopulations
Gnomad4 AFR
AF:
0.269
Gnomad4 AMR
AF:
0.718
Gnomad4 ASJ
AF:
0.541
Gnomad4 EAS
AF:
0.872
Gnomad4 SAS
AF:
0.521
Gnomad4 FIN
AF:
0.671
Gnomad4 NFE
AF:
0.629
Gnomad4 OTH
AF:
0.555
Alfa
AF:
0.583
Hom.:
14981
Bravo
AF:
0.545

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
1.6
DANN
Benign
0.84

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: rs2159767; hg19: chrX-147381021; API