rs1891760

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 0.401 in 151,964 control chromosomes in the GnomAD database, including 13,307 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 0.40 ( 13307 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.20
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=-0.55).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 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:
0.401
AC:
60857
AN:
151846
Hom.:
13295
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.230
Gnomad AMI
AF:
0.442
Gnomad AMR
AF:
0.545
Gnomad ASJ
AF:
0.386
Gnomad EAS
AF:
0.553
Gnomad SAS
AF:
0.588
Gnomad FIN
AF:
0.532
Gnomad MID
AF:
0.290
Gnomad NFE
AF:
0.428
Gnomad OTH
AF:
0.387
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.401
AC:
60886
AN:
151964
Hom.:
13307
Cov.:
31
AF XY:
0.413
AC XY:
30703
AN XY:
74266
show subpopulations
Gnomad4 AFR
AF:
0.230
Gnomad4 AMR
AF:
0.546
Gnomad4 ASJ
AF:
0.386
Gnomad4 EAS
AF:
0.553
Gnomad4 SAS
AF:
0.587
Gnomad4 FIN
AF:
0.532
Gnomad4 NFE
AF:
0.428
Gnomad4 OTH
AF:
0.389
Alfa
AF:
0.423
Hom.:
13431
Bravo
AF:
0.393
Asia WGS
AF:
0.562
AC:
1956
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.55
CADD
Benign
9.5
DANN
Benign
0.55

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: rs1891760; hg19: chr10-115259106; API