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GeneBe

X-93861388-A-G

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 0.159 in 111,050 control chromosomes in the GnomAD database, including 1,164 homozygotes. There are 4,912 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 0.16 ( 1164 hom., 4912 hem., cov: 22)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.494
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=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

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:
0.159
AC:
17607
AN:
110998
Hom.:
1162
Cov.:
22
AF XY:
0.148
AC XY:
4901
AN XY:
33222
show subpopulations
Gnomad AFR
AF:
0.228
Gnomad AMI
AF:
0.176
Gnomad AMR
AF:
0.112
Gnomad ASJ
AF:
0.190
Gnomad EAS
AF:
0.206
Gnomad SAS
AF:
0.107
Gnomad FIN
AF:
0.124
Gnomad MID
AF:
0.0991
Gnomad NFE
AF:
0.130
Gnomad OTH
AF:
0.156
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.159
AC:
17617
AN:
111050
Hom.:
1164
Cov.:
22
AF XY:
0.148
AC XY:
4912
AN XY:
33284
show subpopulations
Gnomad4 AFR
AF:
0.228
Gnomad4 AMR
AF:
0.111
Gnomad4 ASJ
AF:
0.190
Gnomad4 EAS
AF:
0.206
Gnomad4 SAS
AF:
0.107
Gnomad4 FIN
AF:
0.124
Gnomad4 NFE
AF:
0.130
Gnomad4 OTH
AF:
0.155
Alfa
AF:
0.136
Hom.:
3364
Bravo
AF:
0.165

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
3.6
Dann
Benign
0.89

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: rs1797020; hg19: chrX-93116387; API