X-140156297-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 0.47 in 109,686 control chromosomes in the GnomAD database, including 8,852 homozygotes. There are 14,977 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 0.47 ( 8852 hom., 14977 hem., cov: 22)

Consequence

Unknown

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.305
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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 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:
0.470
AC:
51529
AN:
109638
Hom.:
8845
Cov.:
22
AF XY:
0.468
AC XY:
14959
AN XY:
31966
show subpopulations
Gnomad AFR
AF:
0.372
Gnomad AMI
AF:
0.459
Gnomad AMR
AF:
0.501
Gnomad ASJ
AF:
0.460
Gnomad EAS
AF:
0.542
Gnomad SAS
AF:
0.434
Gnomad FIN
AF:
0.510
Gnomad MID
AF:
0.367
Gnomad NFE
AF:
0.514
Gnomad OTH
AF:
0.468
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.470
AC:
51549
AN:
109686
Hom.:
8852
Cov.:
22
AF XY:
0.468
AC XY:
14977
AN XY:
32024
show subpopulations
Gnomad4 AFR
AF:
0.372
Gnomad4 AMR
AF:
0.501
Gnomad4 ASJ
AF:
0.460
Gnomad4 EAS
AF:
0.542
Gnomad4 SAS
AF:
0.433
Gnomad4 FIN
AF:
0.510
Gnomad4 NFE
AF:
0.514
Gnomad4 OTH
AF:
0.473
Alfa
AF:
0.491
Hom.:
3946
Bravo
AF:
0.466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
4.7

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: rs613278; hg19: chrX-139238459; API