rs17027130

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 0.068 in 152,222 control chromosomes in the GnomAD database, including 663 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 0.068 ( 663 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00700
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=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 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:
0.0680
AC:
10348
AN:
152104
Hom.:
659
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0142
Gnomad AMI
AF:
0.0603
Gnomad AMR
AF:
0.115
Gnomad ASJ
AF:
0.0735
Gnomad EAS
AF:
0.357
Gnomad SAS
AF:
0.145
Gnomad FIN
AF:
0.0520
Gnomad MID
AF:
0.0854
Gnomad NFE
AF:
0.0652
Gnomad OTH
AF:
0.0684
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0680
AC:
10354
AN:
152222
Hom.:
663
Cov.:
32
AF XY:
0.0708
AC XY:
5269
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.0142
Gnomad4 AMR
AF:
0.115
Gnomad4 ASJ
AF:
0.0735
Gnomad4 EAS
AF:
0.358
Gnomad4 SAS
AF:
0.145
Gnomad4 FIN
AF:
0.0520
Gnomad4 NFE
AF:
0.0652
Gnomad4 OTH
AF:
0.0687
Alfa
AF:
0.0692
Hom.:
374
Bravo
AF:
0.0697
Asia WGS
AF:
0.214
AC:
743
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.1
DANN
Benign
0.43

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: rs17027130; hg19: chr2-41273631; API