rs17043185

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 0.112 in 152,094 control chromosomes in the GnomAD database, including 1,881 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 0.11 ( 1881 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.918
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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

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:
0.112
AC:
16994
AN:
151976
Hom.:
1877
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.277
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0853
Gnomad ASJ
AF:
0.0230
Gnomad EAS
AF:
0.117
Gnomad SAS
AF:
0.176
Gnomad FIN
AF:
0.0426
Gnomad MID
AF:
0.0924
Gnomad NFE
AF:
0.0298
Gnomad OTH
AF:
0.0915
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.112
AC:
17024
AN:
152094
Hom.:
1881
Cov.:
32
AF XY:
0.113
AC XY:
8420
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.277
Gnomad4 AMR
AF:
0.0854
Gnomad4 ASJ
AF:
0.0230
Gnomad4 EAS
AF:
0.117
Gnomad4 SAS
AF:
0.175
Gnomad4 FIN
AF:
0.0426
Gnomad4 NFE
AF:
0.0298
Gnomad4 OTH
AF:
0.0938
Alfa
AF:
0.0447
Hom.:
367
Bravo
AF:
0.118
Asia WGS
AF:
0.183
AC:
635
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.46
DANN
Benign
0.56

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: rs17043185; hg19: chr2-52896902; API