rs17385675

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 0.0613 in 152,146 control chromosomes in the GnomAD database, including 342 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 0.061 ( 342 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.07
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=-0.95).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0802 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:
0.0614
AC:
9332
AN:
152028
Hom.:
343
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0282
Gnomad AMI
AF:
0.121
Gnomad AMR
AF:
0.0753
Gnomad ASJ
AF:
0.141
Gnomad EAS
AF:
0.00270
Gnomad SAS
AF:
0.0226
Gnomad FIN
AF:
0.0486
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.0820
Gnomad OTH
AF:
0.0793
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0613
AC:
9325
AN:
152146
Hom.:
342
Cov.:
31
AF XY:
0.0595
AC XY:
4429
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.0282
Gnomad4 AMR
AF:
0.0752
Gnomad4 ASJ
AF:
0.141
Gnomad4 EAS
AF:
0.00271
Gnomad4 SAS
AF:
0.0226
Gnomad4 FIN
AF:
0.0486
Gnomad4 NFE
AF:
0.0820
Gnomad4 OTH
AF:
0.0781
Alfa
AF:
0.0799
Hom.:
956
Bravo
AF:
0.0625
Asia WGS
AF:
0.0170
AC:
61
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.0080
DANN
Benign
0.58

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: rs17385675; hg19: chr2-202807196; API