rs9257445

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 0.341 in 151,930 control chromosomes in the GnomAD database, including 10,197 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 0.34 ( 10197 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.19
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=-0.59).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 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:
0.341
AC:
51696
AN:
151812
Hom.:
10176
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.540
Gnomad AMI
AF:
0.208
Gnomad AMR
AF:
0.291
Gnomad ASJ
AF:
0.381
Gnomad EAS
AF:
0.225
Gnomad SAS
AF:
0.363
Gnomad FIN
AF:
0.292
Gnomad MID
AF:
0.259
Gnomad NFE
AF:
0.245
Gnomad OTH
AF:
0.338
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.341
AC:
51754
AN:
151930
Hom.:
10197
Cov.:
32
AF XY:
0.343
AC XY:
25493
AN XY:
74264
show subpopulations
Gnomad4 AFR
AF:
0.541
Gnomad4 AMR
AF:
0.290
Gnomad4 ASJ
AF:
0.381
Gnomad4 EAS
AF:
0.224
Gnomad4 SAS
AF:
0.362
Gnomad4 FIN
AF:
0.292
Gnomad4 NFE
AF:
0.245
Gnomad4 OTH
AF:
0.335
Alfa
AF:
0.295
Hom.:
1027
Bravo
AF:
0.350
Asia WGS
AF:
0.282
AC:
984
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.59
CADD
Benign
0.50
DANN
Benign
0.50

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: rs9257445; hg19: chr6-28949206; API