chrX-80918441-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 0.114 in 110,390 control chromosomes in the GnomAD database, including 1,393 homozygotes. There are 3,524 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 0.11 ( 1393 hom., 3524 hem., cov: 22)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212
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=-0.77).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 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:
0.114
AC:
12578
AN:
110343
Hom.:
1394
Cov.:
22
AF XY:
0.107
AC XY:
3506
AN XY:
32669
show subpopulations
Gnomad AFR
AF:
0.351
Gnomad AMI
AF:
0.00727
Gnomad AMR
AF:
0.0486
Gnomad ASJ
AF:
0.0448
Gnomad EAS
AF:
0.000284
Gnomad SAS
AF:
0.0110
Gnomad FIN
AF:
0.0926
Gnomad MID
AF:
0.0858
Gnomad NFE
AF:
0.0114
Gnomad OTH
AF:
0.0935
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.114
AC:
12600
AN:
110390
Hom.:
1393
Cov.:
22
AF XY:
0.108
AC XY:
3524
AN XY:
32726
show subpopulations
Gnomad4 AFR
AF:
0.351
Gnomad4 AMR
AF:
0.0485
Gnomad4 ASJ
AF:
0.0448
Gnomad4 EAS
AF:
0.000284
Gnomad4 SAS
AF:
0.0111
Gnomad4 FIN
AF:
0.0926
Gnomad4 NFE
AF:
0.0114
Gnomad4 OTH
AF:
0.0917
Alfa
AF:
0.0644
Hom.:
800
Bravo
AF:
0.122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
5.7
DANN
Benign
0.80

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: rs7056400; hg19: chrX-80173940; API