17-48968914-A-G

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 0.542 in 152,006 control chromosomes in the GnomAD database, including 23,992 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 0.54 ( 23992 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.184
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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 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:
0.542
AC:
82294
AN:
151888
Hom.:
23943
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.765
Gnomad AMI
AF:
0.357
Gnomad AMR
AF:
0.543
Gnomad ASJ
AF:
0.455
Gnomad EAS
AF:
0.291
Gnomad SAS
AF:
0.464
Gnomad FIN
AF:
0.460
Gnomad MID
AF:
0.516
Gnomad NFE
AF:
0.451
Gnomad OTH
AF:
0.522
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.542
AC:
82408
AN:
152006
Hom.:
23992
Cov.:
32
AF XY:
0.540
AC XY:
40155
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.765
Gnomad4 AMR
AF:
0.544
Gnomad4 ASJ
AF:
0.455
Gnomad4 EAS
AF:
0.292
Gnomad4 SAS
AF:
0.464
Gnomad4 FIN
AF:
0.460
Gnomad4 NFE
AF:
0.451
Gnomad4 OTH
AF:
0.519
Alfa
AF:
0.512
Hom.:
3383
Bravo
AF:
0.555
Asia WGS
AF:
0.432
AC:
1507
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.2
DANN
Benign
0.66

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: rs937301; hg19: chr17-47046276; API