X-43648052-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 0.62 ( 15855 hom., 19845 hem., cov: 22)
Failed GnomAD Quality Control

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.392
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=-0.91).

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:
0.623
AC:
68496
AN:
109948
Hom.:
15855
Cov.:
22
AF XY:
0.615
AC XY:
19812
AN XY:
32218
show subpopulations
Gnomad AFR
AF:
0.448
Gnomad AMI
AF:
0.665
Gnomad AMR
AF:
0.795
Gnomad ASJ
AF:
0.694
Gnomad EAS
AF:
0.528
Gnomad SAS
AF:
0.427
Gnomad FIN
AF:
0.564
Gnomad MID
AF:
0.703
Gnomad NFE
AF:
0.707
Gnomad OTH
AF:
0.657
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:
0.623
AC:
68526
AN:
110007
Hom.:
15855
Cov.:
22
AF XY:
0.615
AC XY:
19845
AN XY:
32287
show subpopulations
Gnomad4 AFR
AF:
0.447
Gnomad4 AMR
AF:
0.796
Gnomad4 ASJ
AF:
0.694
Gnomad4 EAS
AF:
0.528
Gnomad4 SAS
AF:
0.429
Gnomad4 FIN
AF:
0.564
Gnomad4 NFE
AF:
0.707
Gnomad4 OTH
AF:
0.656
Alfa
AF:
0.697
Hom.:
63165
Bravo
AF:
0.636

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.8
DANN
Benign
0.43

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: rs5905613; hg19: chrX-43507300; API