rs10938397

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 0.374 in 151,772 control chromosomes in the GnomAD database, including 11,281 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 ( 11281 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.745
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 (NFE) allele frequency at 95% confidence interval = 0.427 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:
0.374
AC:
56777
AN:
151654
Hom.:
11280
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.242
Gnomad AMI
AF:
0.319
Gnomad AMR
AF:
0.405
Gnomad ASJ
AF:
0.444
Gnomad EAS
AF:
0.283
Gnomad SAS
AF:
0.391
Gnomad FIN
AF:
0.504
Gnomad MID
AF:
0.378
Gnomad NFE
AF:
0.431
Gnomad OTH
AF:
0.381
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.374
AC:
56787
AN:
151772
Hom.:
11281
Cov.:
32
AF XY:
0.376
AC XY:
27916
AN XY:
74186
show subpopulations
Gnomad4 AFR
AF:
0.242
Gnomad4 AMR
AF:
0.404
Gnomad4 ASJ
AF:
0.444
Gnomad4 EAS
AF:
0.282
Gnomad4 SAS
AF:
0.391
Gnomad4 FIN
AF:
0.504
Gnomad4 NFE
AF:
0.431
Gnomad4 OTH
AF:
0.377
Alfa
AF:
0.415
Hom.:
14122
Bravo
AF:
0.361
Asia WGS
AF:
0.302
AC:
1049
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.2
DANN
Benign
0.67

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: rs10938397; hg19: chr4-45182527; API