rs10036001

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.219 in 152,024 control chromosomes in the GnomAD database, including 3,740 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 0.22 ( 3740 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.252
Variant links:

Genome browser will be placed here

ACMG classification

Our verdict: Benign. The variant received -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 = 0.257 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:
0.219
AC:
33272
AN:
151906
Hom.:
3739
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.203
Gnomad AMI
AF:
0.195
Gnomad AMR
AF:
0.178
Gnomad ASJ
AF:
0.144
Gnomad EAS
AF:
0.268
Gnomad SAS
AF:
0.241
Gnomad FIN
AF:
0.264
Gnomad MID
AF:
0.155
Gnomad NFE
AF:
0.231
Gnomad OTH
AF:
0.172
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.219
AC:
33282
AN:
152024
Hom.:
3740
Cov.:
32
AF XY:
0.222
AC XY:
16526
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.203
AC:
0.202995
AN:
0.202995
Gnomad4 AMR
AF:
0.178
AC:
0.177567
AN:
0.177567
Gnomad4 ASJ
AF:
0.144
AC:
0.143804
AN:
0.143804
Gnomad4 EAS
AF:
0.269
AC:
0.269097
AN:
0.269097
Gnomad4 SAS
AF:
0.241
AC:
0.240964
AN:
0.240964
Gnomad4 FIN
AF:
0.264
AC:
0.264121
AN:
0.264121
Gnomad4 NFE
AF:
0.232
AC:
0.231519
AN:
0.231519
Gnomad4 OTH
AF:
0.171
AC:
0.171402
AN:
0.171402
Heterozygous variant carriers
0
1324
2648
3972
5296
6620
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
354
708
1062
1416
1770
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.221
Hom.:
953
Bravo
AF:
0.210
Asia WGS
AF:
0.226
AC:
784
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
6.0
DANN
Benign
0.73

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: rs10036001; hg19: chr5-5850412; API