rs1932420

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.261 in 152,030 control chromosomes in the GnomAD database, including 5,864 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 0.26 ( 5864 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.145
Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 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:
0.261
AC:
39629
AN:
151912
Hom.:
5879
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.121
Gnomad AMI
AF:
0.170
Gnomad AMR
AF:
0.317
Gnomad ASJ
AF:
0.414
Gnomad EAS
AF:
0.447
Gnomad SAS
AF:
0.324
Gnomad FIN
AF:
0.273
Gnomad MID
AF:
0.535
Gnomad NFE
AF:
0.303
Gnomad OTH
AF:
0.311
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.261
AC:
39622
AN:
152030
Hom.:
5864
Cov.:
32
AF XY:
0.262
AC XY:
19493
AN XY:
74316
show subpopulations
Gnomad4 AFR
AF:
0.122
Gnomad4 AMR
AF:
0.317
Gnomad4 ASJ
AF:
0.414
Gnomad4 EAS
AF:
0.447
Gnomad4 SAS
AF:
0.324
Gnomad4 FIN
AF:
0.273
Gnomad4 NFE
AF:
0.303
Gnomad4 OTH
AF:
0.306
Alfa
AF:
0.290
Hom.:
3237
Bravo
AF:
0.260
Asia WGS
AF:
0.320
AC:
1114
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.28
CADD
Benign
16
DANN
Benign
0.64

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: rs1932420; hg19: chr9-24901567; API