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GeneBe

rs10941679

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 0.254 in 151,982 control chromosomes in the GnomAD database, including 5,365 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 0.25 ( 5365 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.303
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 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:
0.254
AC:
38550
AN:
151864
Hom.:
5344
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.189
Gnomad AMI
AF:
0.248
Gnomad AMR
AF:
0.340
Gnomad ASJ
AF:
0.170
Gnomad EAS
AF:
0.499
Gnomad SAS
AF:
0.365
Gnomad FIN
AF:
0.254
Gnomad MID
AF:
0.252
Gnomad NFE
AF:
0.252
Gnomad OTH
AF:
0.260
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.254
AC:
38596
AN:
151982
Hom.:
5365
Cov.:
32
AF XY:
0.260
AC XY:
19313
AN XY:
74278
show subpopulations
Gnomad4 AFR
AF:
0.189
Gnomad4 AMR
AF:
0.341
Gnomad4 ASJ
AF:
0.170
Gnomad4 EAS
AF:
0.499
Gnomad4 SAS
AF:
0.366
Gnomad4 FIN
AF:
0.254
Gnomad4 NFE
AF:
0.252
Gnomad4 OTH
AF:
0.267
Alfa
AF:
0.257
Hom.:
2386
Bravo
AF:
0.257
Asia WGS
AF:
0.431
AC:
1497
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
3.3
Dann
Benign
0.43

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: rs10941679; hg19: chr5-44706498; API