rs6892289

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 0.135 in 152,226 control chromosomes in the GnomAD database, including 1,521 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 0.14 ( 1521 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0890
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=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 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:
0.135
AC:
20569
AN:
152108
Hom.:
1522
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.153
Gnomad AMI
AF:
0.0603
Gnomad AMR
AF:
0.152
Gnomad ASJ
AF:
0.237
Gnomad EAS
AF:
0.0328
Gnomad SAS
AF:
0.152
Gnomad FIN
AF:
0.0612
Gnomad MID
AF:
0.285
Gnomad NFE
AF:
0.133
Gnomad OTH
AF:
0.168
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.135
AC:
20581
AN:
152226
Hom.:
1521
Cov.:
33
AF XY:
0.131
AC XY:
9760
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.152
Gnomad4 AMR
AF:
0.151
Gnomad4 ASJ
AF:
0.237
Gnomad4 EAS
AF:
0.0330
Gnomad4 SAS
AF:
0.152
Gnomad4 FIN
AF:
0.0612
Gnomad4 NFE
AF:
0.133
Gnomad4 OTH
AF:
0.168
Alfa
AF:
0.142
Hom.:
2217
Bravo
AF:
0.142
Asia WGS
AF:
0.0990
AC:
343
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
2.1
DANN
Benign
0.42

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: rs6892289; hg19: chr5-82070913; API