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GeneBe

rs1927914

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 0.531 in 152,050 control chromosomes in the GnomAD database, including 24,124 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 0.53 ( 24124 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.161
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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 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
AF:
0.532
AC:
80777
AN:
151932
Hom.:
24131
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.234
Gnomad AMI
AF:
0.758
Gnomad AMR
AF:
0.614
Gnomad ASJ
AF:
0.628
Gnomad EAS
AF:
0.619
Gnomad SAS
AF:
0.617
Gnomad FIN
AF:
0.551
Gnomad MID
AF:
0.653
Gnomad NFE
AF:
0.668
Gnomad OTH
AF:
0.582
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.531
AC:
80786
AN:
152050
Hom.:
24124
Cov.:
32
AF XY:
0.530
AC XY:
39379
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.234
Gnomad4 AMR
AF:
0.614
Gnomad4 ASJ
AF:
0.628
Gnomad4 EAS
AF:
0.619
Gnomad4 SAS
AF:
0.616
Gnomad4 FIN
AF:
0.551
Gnomad4 NFE
AF:
0.668
Gnomad4 OTH
AF:
0.579
Alfa
AF:
0.636
Hom.:
14425
Bravo
AF:
0.527
Asia WGS
AF:
0.594
AC:
2067
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.4
DANN
Benign
0.43

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: rs1927914; hg19: chr9-120464725; API