rs928722

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 152,108 control chromosomes in the GnomAD database, including 2,132 homozygotes. 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 ( 2132 hom., cov: 31)

Consequence

Unknown

Scores

2

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=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 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:
0.159
AC:
24190
AN:
151990
Hom.:
2131
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.110
Gnomad AMI
AF:
0.157
Gnomad AMR
AF:
0.124
Gnomad ASJ
AF:
0.150
Gnomad EAS
AF:
0.00193
Gnomad SAS
AF:
0.121
Gnomad FIN
AF:
0.178
Gnomad MID
AF:
0.139
Gnomad NFE
AF:
0.209
Gnomad OTH
AF:
0.161
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.159
AC:
24195
AN:
152108
Hom.:
2132
Cov.:
31
AF XY:
0.155
AC XY:
11503
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.110
Gnomad4 AMR
AF:
0.124
Gnomad4 ASJ
AF:
0.150
Gnomad4 EAS
AF:
0.00193
Gnomad4 SAS
AF:
0.121
Gnomad4 FIN
AF:
0.178
Gnomad4 NFE
AF:
0.209
Gnomad4 OTH
AF:
0.160
Alfa
AF:
0.181
Hom.:
336
Bravo
AF:
0.153
Asia WGS
AF:
0.0610
AC:
213
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
7.2
DANN
Benign
0.58

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: rs928722; hg19: chr6-137973832; API