chr9-85238445-G-A

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 0.695 in 151,994 control chromosomes in the GnomAD database, including 38,645 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 0.70 ( 38645 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.724
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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.908 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:
0.695
AC:
105571
AN:
151876
Hom.:
38578
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.916
Gnomad AMI
AF:
0.349
Gnomad AMR
AF:
0.683
Gnomad ASJ
AF:
0.621
Gnomad EAS
AF:
0.882
Gnomad SAS
AF:
0.707
Gnomad FIN
AF:
0.643
Gnomad MID
AF:
0.694
Gnomad NFE
AF:
0.565
Gnomad OTH
AF:
0.699
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.695
AC:
105697
AN:
151994
Hom.:
38645
Cov.:
32
AF XY:
0.699
AC XY:
51954
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.916
Gnomad4 AMR
AF:
0.683
Gnomad4 ASJ
AF:
0.621
Gnomad4 EAS
AF:
0.882
Gnomad4 SAS
AF:
0.707
Gnomad4 FIN
AF:
0.643
Gnomad4 NFE
AF:
0.565
Gnomad4 OTH
AF:
0.703
Alfa
AF:
0.593
Hom.:
11412
Bravo
AF:
0.711
Asia WGS
AF:
0.799
AC:
2770
AN:
3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
4.6
DANN
Benign
0.68

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: rs7040848; hg19: chr9-87853360; API