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GeneBe

rs10938397

chr4-45180510-A-G

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 151654 control chromosomes in the gnomAD Genomes database, including 11280 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 ( 11280 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.745

Links

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 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:
0.374
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
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
0.41
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;