rs2326689

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 0.189 in 152,136 control chromosomes in the GnomAD database, including 2,848 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 0.19 ( 2848 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0500
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 (EAS) allele frequency at 95% confidence interval = 0.209 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:
0.189
AC:
28773
AN:
152018
Hom.:
2848
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.212
Gnomad AMI
AF:
0.216
Gnomad AMR
AF:
0.176
Gnomad ASJ
AF:
0.251
Gnomad EAS
AF:
0.214
Gnomad SAS
AF:
0.137
Gnomad FIN
AF:
0.131
Gnomad MID
AF:
0.256
Gnomad NFE
AF:
0.186
Gnomad OTH
AF:
0.171
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.189
AC:
28795
AN:
152136
Hom.:
2848
Cov.:
32
AF XY:
0.186
AC XY:
13830
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.212
Gnomad4 AMR
AF:
0.176
Gnomad4 ASJ
AF:
0.251
Gnomad4 EAS
AF:
0.214
Gnomad4 SAS
AF:
0.137
Gnomad4 FIN
AF:
0.131
Gnomad4 NFE
AF:
0.186
Gnomad4 OTH
AF:
0.169
Alfa
AF:
0.183
Hom.:
1453
Bravo
AF:
0.196
Asia WGS
AF:
0.169
AC:
592
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
1.0
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: rs2326689; hg19: chr6-6021878; API