rs17347854

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 0.125 in 152,106 control chromosomes in the GnomAD database, including 1,255 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 0.13 ( 1255 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.839
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=-0.84).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.147 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:
0.125
AC:
19032
AN:
151988
Hom.:
1255
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0928
Gnomad AMI
AF:
0.170
Gnomad AMR
AF:
0.132
Gnomad ASJ
AF:
0.158
Gnomad EAS
AF:
0.0535
Gnomad SAS
AF:
0.133
Gnomad FIN
AF:
0.0978
Gnomad MID
AF:
0.199
Gnomad NFE
AF:
0.150
Gnomad OTH
AF:
0.133
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.125
AC:
19050
AN:
152106
Hom.:
1255
Cov.:
32
AF XY:
0.125
AC XY:
9265
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.0929
Gnomad4 AMR
AF:
0.132
Gnomad4 ASJ
AF:
0.158
Gnomad4 EAS
AF:
0.0536
Gnomad4 SAS
AF:
0.132
Gnomad4 FIN
AF:
0.0978
Gnomad4 NFE
AF:
0.150
Gnomad4 OTH
AF:
0.134
Alfa
AF:
0.146
Hom.:
2166
Bravo
AF:
0.123
Asia WGS
AF:
0.0980
AC:
340
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
5.2
DANN
Benign
0.81

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: rs17347854; hg19: chr11-11247842; API