rs2326510

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 0.366 in 151,972 control chromosomes in the GnomAD database, including 12,718 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 0.37 ( 12718 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.58
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 (AFR) allele frequency at 95% confidence interval = 0.645 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:
0.365
AC:
55455
AN:
151854
Hom.:
12673
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.651
Gnomad AMI
AF:
0.311
Gnomad AMR
AF:
0.343
Gnomad ASJ
AF:
0.354
Gnomad EAS
AF:
0.0820
Gnomad SAS
AF:
0.262
Gnomad FIN
AF:
0.284
Gnomad MID
AF:
0.301
Gnomad NFE
AF:
0.241
Gnomad OTH
AF:
0.330
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.366
AC:
55568
AN:
151972
Hom.:
12718
Cov.:
32
AF XY:
0.365
AC XY:
27134
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.651
Gnomad4 AMR
AF:
0.343
Gnomad4 ASJ
AF:
0.354
Gnomad4 EAS
AF:
0.0824
Gnomad4 SAS
AF:
0.262
Gnomad4 FIN
AF:
0.284
Gnomad4 NFE
AF:
0.241
Gnomad4 OTH
AF:
0.328
Alfa
AF:
0.262
Hom.:
9689
Bravo
AF:
0.381
Asia WGS
AF:
0.191
AC:
667
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.12
DANN
Benign
0.35

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: rs2326510; hg19: chr20-4701211; API