rs230989

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 0.227 in 152,044 control chromosomes in the GnomAD database, including 4,299 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 0.23 ( 4299 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.293
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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.268 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:
0.227
AC:
34506
AN:
151926
Hom.:
4299
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.134
Gnomad AMI
AF:
0.361
Gnomad AMR
AF:
0.268
Gnomad ASJ
AF:
0.278
Gnomad EAS
AF:
0.173
Gnomad SAS
AF:
0.147
Gnomad FIN
AF:
0.276
Gnomad MID
AF:
0.177
Gnomad NFE
AF:
0.272
Gnomad OTH
AF:
0.253
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.227
AC:
34497
AN:
152044
Hom.:
4299
Cov.:
31
AF XY:
0.225
AC XY:
16702
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.134
Gnomad4 AMR
AF:
0.268
Gnomad4 ASJ
AF:
0.278
Gnomad4 EAS
AF:
0.173
Gnomad4 SAS
AF:
0.147
Gnomad4 FIN
AF:
0.276
Gnomad4 NFE
AF:
0.271
Gnomad4 OTH
AF:
0.250
Alfa
AF:
0.264
Hom.:
7815
Bravo
AF:
0.224
Asia WGS
AF:
0.155
AC:
537
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.7
DANN
Benign
0.50

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: rs230989; hg19: chr17-15113435; API