rs10518275

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 0.155 in 152,212 control chromosomes in the GnomAD database, including 2,178 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 0.16 ( 2178 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.11
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=-0.89).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.249 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:
0.155
AC:
23638
AN:
152094
Hom.:
2170
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0842
Gnomad AMI
AF:
0.212
Gnomad AMR
AF:
0.254
Gnomad ASJ
AF:
0.134
Gnomad EAS
AF:
0.00250
Gnomad SAS
AF:
0.0546
Gnomad FIN
AF:
0.184
Gnomad MID
AF:
0.152
Gnomad NFE
AF:
0.190
Gnomad OTH
AF:
0.187
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.155
AC:
23664
AN:
152212
Hom.:
2178
Cov.:
33
AF XY:
0.155
AC XY:
11555
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.0841
Gnomad4 AMR
AF:
0.255
Gnomad4 ASJ
AF:
0.134
Gnomad4 EAS
AF:
0.00251
Gnomad4 SAS
AF:
0.0557
Gnomad4 FIN
AF:
0.184
Gnomad4 NFE
AF:
0.190
Gnomad4 OTH
AF:
0.184
Alfa
AF:
0.175
Hom.:
1441
Bravo
AF:
0.160
Asia WGS
AF:
0.0410
AC:
144
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
6.3
DANN
Benign
0.76

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: rs10518275; hg19: chr19-33850841; API