rs10516147

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 0.206 in 152,130 control chromosomes in the GnomAD database, including 3,832 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 0.21 ( 3832 hom., cov: 32)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.58
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.178667483A>G intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.206
AC:
31271
AN:
152012
Hom.:
3832
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0785
Gnomad AMI
AF:
0.192
Gnomad AMR
AF:
0.238
Gnomad ASJ
AF:
0.187
Gnomad EAS
AF:
0.375
Gnomad SAS
AF:
0.335
Gnomad FIN
AF:
0.358
Gnomad MID
AF:
0.234
Gnomad NFE
AF:
0.232
Gnomad OTH
AF:
0.199
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.206
AC:
31281
AN:
152130
Hom.:
3832
Cov.:
32
AF XY:
0.215
AC XY:
15991
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.0784
Gnomad4 AMR
AF:
0.237
Gnomad4 ASJ
AF:
0.187
Gnomad4 EAS
AF:
0.375
Gnomad4 SAS
AF:
0.336
Gnomad4 FIN
AF:
0.358
Gnomad4 NFE
AF:
0.232
Gnomad4 OTH
AF:
0.204
Alfa
AF:
0.225
Hom.:
4851
Bravo
AF:
0.186
Asia WGS
AF:
0.370
AC:
1290
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.88
DANN
Benign
0.28

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: rs10516147; hg19: chr5-178094484; COSMIC: COSV60238739; API