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GeneBe

rs1018910

Positions:

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 0.326 in 152,086 control chromosomes in the GnomAD database, including 8,877 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 0.33 ( 8877 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.215
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.447 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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.326
AC:
49560
AN:
151968
Hom.:
8840
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.447
Gnomad AMI
AF:
0.224
Gnomad AMR
AF:
0.455
Gnomad ASJ
AF:
0.298
Gnomad EAS
AF:
0.238
Gnomad SAS
AF:
0.214
Gnomad FIN
AF:
0.226
Gnomad MID
AF:
0.342
Gnomad NFE
AF:
0.257
Gnomad OTH
AF:
0.311
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.326
AC:
49652
AN:
152086
Hom.:
8877
Cov.:
32
AF XY:
0.325
AC XY:
24135
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.448
Gnomad4 AMR
AF:
0.456
Gnomad4 ASJ
AF:
0.298
Gnomad4 EAS
AF:
0.237
Gnomad4 SAS
AF:
0.213
Gnomad4 FIN
AF:
0.226
Gnomad4 NFE
AF:
0.257
Gnomad4 OTH
AF:
0.316
Alfa
AF:
0.310
Hom.:
1404
Bravo
AF:
0.353
Asia WGS
AF:
0.289
AC:
1005
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
9.8
DANN
Benign
0.72

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: rs1018910; hg19: chr16-71278468; API