rs2038596

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 0.803 in 152,172 control chromosomes in the GnomAD database, including 49,482 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 0.80 ( 49482 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.662
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=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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:
0.802
AC:
122001
AN:
152052
Hom.:
49422
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.875
Gnomad AMI
AF:
0.703
Gnomad AMR
AF:
0.820
Gnomad ASJ
AF:
0.760
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.925
Gnomad FIN
AF:
0.773
Gnomad MID
AF:
0.769
Gnomad NFE
AF:
0.740
Gnomad OTH
AF:
0.779
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.803
AC:
122122
AN:
152172
Hom.:
49482
Cov.:
31
AF XY:
0.808
AC XY:
60130
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.874
Gnomad4 AMR
AF:
0.820
Gnomad4 ASJ
AF:
0.760
Gnomad4 EAS
AF:
0.999
Gnomad4 SAS
AF:
0.926
Gnomad4 FIN
AF:
0.773
Gnomad4 NFE
AF:
0.740
Gnomad4 OTH
AF:
0.782
Alfa
AF:
0.769
Hom.:
5639
Bravo
AF:
0.811
Asia WGS
AF:
0.953
AC:
3313
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.19
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: rs2038596; hg19: chr10-124114152; API