rs10501828

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 0.612 in 152,196 control chromosomes in the GnomAD database, including 30,222 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 0.61 ( 30222 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.958
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 (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.612
AC:
93093
AN:
152078
Hom.:
30171
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.829
Gnomad AMI
AF:
0.399
Gnomad AMR
AF:
0.643
Gnomad ASJ
AF:
0.615
Gnomad EAS
AF:
0.629
Gnomad SAS
AF:
0.582
Gnomad FIN
AF:
0.461
Gnomad MID
AF:
0.636
Gnomad NFE
AF:
0.500
Gnomad OTH
AF:
0.616
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.612
AC:
93208
AN:
152196
Hom.:
30222
Cov.:
33
AF XY:
0.612
AC XY:
45541
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.830
Gnomad4 AMR
AF:
0.644
Gnomad4 ASJ
AF:
0.615
Gnomad4 EAS
AF:
0.629
Gnomad4 SAS
AF:
0.582
Gnomad4 FIN
AF:
0.461
Gnomad4 NFE
AF:
0.500
Gnomad4 OTH
AF:
0.614
Alfa
AF:
0.487
Hom.:
2379
Bravo
AF:
0.636
Asia WGS
AF:
0.639
AC:
2218
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.11
DANN
Benign
0.41

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: rs10501828; hg19: chr11-95244209; API