chr10-46054955-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 0.454 in 151,460 control chromosomes in the GnomAD database, including 17,243 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 0.45 ( 17243 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.231
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=-0.84).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.543 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:
0.454
AC:
68786
AN:
151348
Hom.:
17250
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.227
Gnomad AMI
AF:
0.489
Gnomad AMR
AF:
0.540
Gnomad ASJ
AF:
0.449
Gnomad EAS
AF:
0.521
Gnomad SAS
AF:
0.413
Gnomad FIN
AF:
0.610
Gnomad MID
AF:
0.339
Gnomad NFE
AF:
0.548
Gnomad OTH
AF:
0.462
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.454
AC:
68778
AN:
151460
Hom.:
17243
Cov.:
30
AF XY:
0.456
AC XY:
33693
AN XY:
73942
show subpopulations
Gnomad4 AFR
AF:
0.227
Gnomad4 AMR
AF:
0.540
Gnomad4 ASJ
AF:
0.449
Gnomad4 EAS
AF:
0.520
Gnomad4 SAS
AF:
0.413
Gnomad4 FIN
AF:
0.610
Gnomad4 NFE
AF:
0.548
Gnomad4 OTH
AF:
0.457
Alfa
AF:
0.510
Hom.:
2612
Bravo
AF:
0.445
Asia WGS
AF:
0.409
AC:
1423
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
6.6
DANN
Benign
0.94

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: rs4630243; hg19: chr10-51540867; API