X-43753072-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 0.0691 in 112,125 control chromosomes in the GnomAD database, including 285 homozygotes. There are 2,232 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 0.069 ( 285 hom., 2232 hem., cov: 23)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.997
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=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0691
AC:
7749
AN:
112075
Hom.:
285
Cov.:
23
AF XY:
0.0652
AC XY:
2232
AN XY:
34249
show subpopulations
Gnomad AFR
AF:
0.0191
Gnomad AMI
AF:
0.183
Gnomad AMR
AF:
0.0422
Gnomad ASJ
AF:
0.0476
Gnomad EAS
AF:
0.000837
Gnomad SAS
AF:
0.0143
Gnomad FIN
AF:
0.116
Gnomad MID
AF:
0.00420
Gnomad NFE
AF:
0.106
Gnomad OTH
AF:
0.0445
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0691
AC:
7750
AN:
112125
Hom.:
285
Cov.:
23
AF XY:
0.0651
AC XY:
2232
AN XY:
34309
show subpopulations
Gnomad4 AFR
AF:
0.0190
Gnomad4 AMR
AF:
0.0422
Gnomad4 ASJ
AF:
0.0476
Gnomad4 EAS
AF:
0.000840
Gnomad4 SAS
AF:
0.0143
Gnomad4 FIN
AF:
0.116
Gnomad4 NFE
AF:
0.106
Gnomad4 OTH
AF:
0.0439
Alfa
AF:
0.0556
Hom.:
376
Bravo
AF:
0.0608

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.28
DANN
Benign
0.72

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: rs12843533; hg19: chrX-43612319; API