rs17527054

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBS1BS2

The variant allele was found at a frequency of 0.0164 in 152,300 control chromosomes in the GnomAD database, including 27 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 0.016 ( 27 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.17
Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0164 (2499/152300) while in subpopulation NFE AF= 0.0298 (2030/68024). AF 95% confidence interval is 0.0288. There are 27 homozygotes in gnomad4. There are 1120 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 27 gene

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:
0.0164
AC:
2499
AN:
152182
Hom.:
27
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00444
Gnomad AMI
AF:
0.0121
Gnomad AMR
AF:
0.00851
Gnomad ASJ
AF:
0.0104
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00456
Gnomad FIN
AF:
0.00612
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0298
Gnomad OTH
AF:
0.00956
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0164
AC:
2499
AN:
152300
Hom.:
27
Cov.:
32
AF XY:
0.0150
AC XY:
1120
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.00443
Gnomad4 AMR
AF:
0.00850
Gnomad4 ASJ
AF:
0.0104
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00456
Gnomad4 FIN
AF:
0.00612
Gnomad4 NFE
AF:
0.0298
Gnomad4 OTH
AF:
0.00946
Alfa
AF:
0.0242
Hom.:
7
Bravo
AF:
0.0155
Asia WGS
AF:
0.00260
AC:
9
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.44
CADD
Benign
11
DANN
Benign
0.67

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: rs17527054; hg19: chr6-23925921; API