rs2369646

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 0.262 in 109,556 control chromosomes in the GnomAD database, including 3,013 homozygotes. There are 8,343 hemizygotes in GnomAD. 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 0.26 ( 3013 hom., 8343 hem., cov: 22)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.140
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=-0.91).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.37 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:
0.262
AC:
28684
AN:
109506
Hom.:
3008
Cov.:
22
AF XY:
0.260
AC XY:
8328
AN XY:
32080
show subpopulations
Gnomad AFR
AF:
0.355
Gnomad AMI
AF:
0.341
Gnomad AMR
AF:
0.379
Gnomad ASJ
AF:
0.221
Gnomad EAS
AF:
0.0606
Gnomad SAS
AF:
0.202
Gnomad FIN
AF:
0.221
Gnomad MID
AF:
0.199
Gnomad NFE
AF:
0.208
Gnomad OTH
AF:
0.251
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.262
AC:
28707
AN:
109556
Hom.:
3013
Cov.:
22
AF XY:
0.260
AC XY:
8343
AN XY:
32140
show subpopulations
Gnomad4 AFR
AF:
0.354
Gnomad4 AMR
AF:
0.380
Gnomad4 ASJ
AF:
0.221
Gnomad4 EAS
AF:
0.0602
Gnomad4 SAS
AF:
0.203
Gnomad4 FIN
AF:
0.221
Gnomad4 NFE
AF:
0.208
Gnomad4 OTH
AF:
0.249
Alfa
AF:
0.220
Hom.:
16745
Bravo
AF:
0.282

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
2.8
DANN
Benign
0.58

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: rs2369646; hg19: chrX-86470056; API