rs1701926

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 0.85 in 152,198 control chromosomes in the GnomAD database, including 56,226 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 0.85 ( 56226 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.304
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=-1.03).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.931 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:
0.850
AC:
129230
AN:
152080
Hom.:
56176
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.939
Gnomad AMI
AF:
0.886
Gnomad AMR
AF:
0.833
Gnomad ASJ
AF:
0.900
Gnomad EAS
AF:
0.224
Gnomad SAS
AF:
0.734
Gnomad FIN
AF:
0.831
Gnomad MID
AF:
0.934
Gnomad NFE
AF:
0.854
Gnomad OTH
AF:
0.871
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.850
AC:
129340
AN:
152198
Hom.:
56226
Cov.:
32
AF XY:
0.844
AC XY:
62825
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.939
Gnomad4 AMR
AF:
0.832
Gnomad4 ASJ
AF:
0.900
Gnomad4 EAS
AF:
0.225
Gnomad4 SAS
AF:
0.734
Gnomad4 FIN
AF:
0.831
Gnomad4 NFE
AF:
0.854
Gnomad4 OTH
AF:
0.868
Alfa
AF:
0.858
Hom.:
7022
Bravo
AF:
0.852
Asia WGS
AF:
0.525
AC:
1830
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.58
DANN
Benign
0.12

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: rs1701926; hg19: chr19-51408758; API