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/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE 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