rs10503564

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000664439.1(ENSG00000287476):​n.163+16520G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0919 in 152,188 control chromosomes in the GnomAD database, including 1,439 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 0.092 ( 1439 hom., cov: 33)

Consequence

ENSG00000287476
ENST00000664439.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.787
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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 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
ENSG00000287476ENST00000664439.1 linkn.163+16520G>A intron_variant Intron 2 of 4

Frequencies

GnomAD3 genomes
AF:
0.0917
AC:
13941
AN:
152070
Hom.:
1429
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.240
Gnomad AMI
AF:
0.0132
Gnomad AMR
AF:
0.127
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.149
Gnomad SAS
AF:
0.0773
Gnomad FIN
AF:
0.00886
Gnomad MID
AF:
0.0190
Gnomad NFE
AF:
0.0101
Gnomad OTH
AF:
0.0692
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0919
AC:
13988
AN:
152188
Hom.:
1439
Cov.:
33
AF XY:
0.0913
AC XY:
6794
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.240
Gnomad4 AMR
AF:
0.127
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.149
Gnomad4 SAS
AF:
0.0765
Gnomad4 FIN
AF:
0.00886
Gnomad4 NFE
AF:
0.0101
Gnomad4 OTH
AF:
0.0690
Alfa
AF:
0.0418
Hom.:
109
Bravo
AF:
0.110
Asia WGS
AF:
0.117
AC:
406
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.25
DANN
Benign
0.44

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: rs10503564; hg19: chr8-15806334; API