rs223886

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 0.628 in 151,654 control chromosomes in the GnomAD database, including 32,361 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 0.63 ( 32361 hom., cov: 29)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.626
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 (NFE) allele frequency at 95% confidence interval = 0.76 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:
0.628
AC:
95117
AN:
151536
Hom.:
32345
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.360
Gnomad AMI
AF:
0.713
Gnomad AMR
AF:
0.631
Gnomad ASJ
AF:
0.720
Gnomad EAS
AF:
0.532
Gnomad SAS
AF:
0.525
Gnomad FIN
AF:
0.838
Gnomad MID
AF:
0.608
Gnomad NFE
AF:
0.765
Gnomad OTH
AF:
0.649
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.628
AC:
95172
AN:
151654
Hom.:
32361
Cov.:
29
AF XY:
0.626
AC XY:
46418
AN XY:
74096
show subpopulations
Gnomad4 AFR
AF:
0.360
Gnomad4 AMR
AF:
0.631
Gnomad4 ASJ
AF:
0.720
Gnomad4 EAS
AF:
0.532
Gnomad4 SAS
AF:
0.525
Gnomad4 FIN
AF:
0.838
Gnomad4 NFE
AF:
0.765
Gnomad4 OTH
AF:
0.653
Alfa
AF:
0.698
Hom.:
4623
Bravo
AF:
0.603
Asia WGS
AF:
0.518
AC:
1802
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
4.4
DANN
Benign
0.44

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: rs223886; hg19: chr16-57389826; API