rs785787

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 0.109 in 111,132 control chromosomes in the GnomAD database, including 685 homozygotes. There are 3,683 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 ( 685 hom., 3683 hem., cov: 22)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.228
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=-0.96).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.335 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:
0.109
AC:
12140
AN:
111081
Hom.:
684
Cov.:
22
AF XY:
0.110
AC XY:
3662
AN XY:
33367
show subpopulations
Gnomad AFR
AF:
0.132
Gnomad AMI
AF:
0.0219
Gnomad AMR
AF:
0.202
Gnomad ASJ
AF:
0.0617
Gnomad EAS
AF:
0.281
Gnomad SAS
AF:
0.354
Gnomad FIN
AF:
0.0350
Gnomad MID
AF:
0.0851
Gnomad NFE
AF:
0.0662
Gnomad OTH
AF:
0.109
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.109
AC:
12163
AN:
111132
Hom.:
685
Cov.:
22
AF XY:
0.110
AC XY:
3683
AN XY:
33428
show subpopulations
Gnomad4 AFR
AF:
0.132
Gnomad4 AMR
AF:
0.203
Gnomad4 ASJ
AF:
0.0617
Gnomad4 EAS
AF:
0.282
Gnomad4 SAS
AF:
0.354
Gnomad4 FIN
AF:
0.0350
Gnomad4 NFE
AF:
0.0662
Gnomad4 OTH
AF:
0.114
Alfa
AF:
0.0130
Hom.:
50
Bravo
AF:
0.120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
3.2
DANN
Benign
0.32

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: rs785787; hg19: chrX-92327255; API