rs150892

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 0.424 in 151,962 control chromosomes in the GnomAD database, including 14,762 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 0.42 ( 14762 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.327
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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.425
AC:
64492
AN:
151844
Hom.:
14763
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.287
Gnomad AMI
AF:
0.586
Gnomad AMR
AF:
0.402
Gnomad ASJ
AF:
0.447
Gnomad EAS
AF:
0.0978
Gnomad SAS
AF:
0.480
Gnomad FIN
AF:
0.580
Gnomad MID
AF:
0.468
Gnomad NFE
AF:
0.507
Gnomad OTH
AF:
0.438
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.424
AC:
64504
AN:
151962
Hom.:
14762
Cov.:
32
AF XY:
0.426
AC XY:
31632
AN XY:
74266
show subpopulations
Gnomad4 AFR
AF:
0.287
Gnomad4 AMR
AF:
0.401
Gnomad4 ASJ
AF:
0.447
Gnomad4 EAS
AF:
0.0978
Gnomad4 SAS
AF:
0.479
Gnomad4 FIN
AF:
0.580
Gnomad4 NFE
AF:
0.507
Gnomad4 OTH
AF:
0.437
Alfa
AF:
0.488
Hom.:
34422
Bravo
AF:
0.404
Asia WGS
AF:
0.281
AC:
976
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.4
DANN
Benign
0.30

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: rs150892; hg19: chr1-96516252; API