rs9273373

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 0.568 in 151,310 control chromosomes in the GnomAD database, including 24,732 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 0.57 ( 24732 hom., cov: 28)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.935
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=-0.89).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.642 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:
0.569
AC:
85959
AN:
151194
Hom.:
24724
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.516
Gnomad AMI
AF:
0.597
Gnomad AMR
AF:
0.652
Gnomad ASJ
AF:
0.628
Gnomad EAS
AF:
0.607
Gnomad SAS
AF:
0.509
Gnomad FIN
AF:
0.517
Gnomad MID
AF:
0.710
Gnomad NFE
AF:
0.586
Gnomad OTH
AF:
0.587
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.568
AC:
86014
AN:
151310
Hom.:
24732
Cov.:
28
AF XY:
0.565
AC XY:
41779
AN XY:
73888
show subpopulations
Gnomad4 AFR
AF:
0.516
Gnomad4 AMR
AF:
0.653
Gnomad4 ASJ
AF:
0.628
Gnomad4 EAS
AF:
0.608
Gnomad4 SAS
AF:
0.508
Gnomad4 FIN
AF:
0.517
Gnomad4 NFE
AF:
0.586
Gnomad4 OTH
AF:
0.583
Alfa
AF:
0.585
Hom.:
2807
Bravo
AF:
0.584

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.7
DANN
Benign
0.86

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: rs9273373; hg19: chr6-32626601; API