rs9912168

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 0.39 in 151,916 control chromosomes in the GnomAD database, including 12,373 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 0.39 ( 12373 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.407
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=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.390
AC:
59250
AN:
151798
Hom.:
12354
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.534
Gnomad AMI
AF:
0.517
Gnomad AMR
AF:
0.399
Gnomad ASJ
AF:
0.404
Gnomad EAS
AF:
0.181
Gnomad SAS
AF:
0.338
Gnomad FIN
AF:
0.328
Gnomad MID
AF:
0.345
Gnomad NFE
AF:
0.329
Gnomad OTH
AF:
0.384
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.390
AC:
59322
AN:
151916
Hom.:
12373
Cov.:
31
AF XY:
0.390
AC XY:
28939
AN XY:
74228
show subpopulations
Gnomad4 AFR
AF:
0.534
Gnomad4 AMR
AF:
0.399
Gnomad4 ASJ
AF:
0.404
Gnomad4 EAS
AF:
0.181
Gnomad4 SAS
AF:
0.337
Gnomad4 FIN
AF:
0.328
Gnomad4 NFE
AF:
0.329
Gnomad4 OTH
AF:
0.382
Alfa
AF:
0.348
Hom.:
12582
Bravo
AF:
0.402
Asia WGS
AF:
0.297
AC:
1032
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.2
DANN
Benign
0.17

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: rs9912168; hg19: chr17-4323294; API