rs900400

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 0.365 in 152,188 control chromosomes in the GnomAD database, including 10,667 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 0.37 ( 10667 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.106
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=-0.68).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 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:
0.365
AC:
55574
AN:
152070
Hom.:
10672
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.262
Gnomad AMI
AF:
0.404
Gnomad AMR
AF:
0.424
Gnomad ASJ
AF:
0.513
Gnomad EAS
AF:
0.504
Gnomad SAS
AF:
0.259
Gnomad FIN
AF:
0.312
Gnomad MID
AF:
0.459
Gnomad NFE
AF:
0.411
Gnomad OTH
AF:
0.412
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.365
AC:
55589
AN:
152188
Hom.:
10667
Cov.:
33
AF XY:
0.361
AC XY:
26841
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.262
Gnomad4 AMR
AF:
0.424
Gnomad4 ASJ
AF:
0.513
Gnomad4 EAS
AF:
0.503
Gnomad4 SAS
AF:
0.258
Gnomad4 FIN
AF:
0.312
Gnomad4 NFE
AF:
0.411
Gnomad4 OTH
AF:
0.409
Alfa
AF:
0.416
Hom.:
5974
Bravo
AF:
0.373
Asia WGS
AF:
0.354
AC:
1226
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
3.5
DANN
Benign
0.88

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: rs900400; hg19: chr3-156798775; API