rs10508717

Variant summary

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

The ENST00000646813.1(ENSG00000284951):​n.630-2921C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,858 control chromosomes in the GnomAD database, including 11,721 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 0.38 ( 11721 hom., cov: 33)

Consequence

ENSG00000284951
ENST00000646813.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.42
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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 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
ENSG00000284951ENST00000646813.1 linkn.630-2921C>T intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.380
AC:
57612
AN:
151750
Hom.:
11726
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.250
Gnomad AMI
AF:
0.365
Gnomad AMR
AF:
0.411
Gnomad ASJ
AF:
0.600
Gnomad EAS
AF:
0.209
Gnomad SAS
AF:
0.382
Gnomad FIN
AF:
0.384
Gnomad MID
AF:
0.516
Gnomad NFE
AF:
0.451
Gnomad OTH
AF:
0.415
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.379
AC:
57607
AN:
151858
Hom.:
11721
Cov.:
33
AF XY:
0.374
AC XY:
27791
AN XY:
74230
show subpopulations
Gnomad4 AFR
AF:
0.249
Gnomad4 AMR
AF:
0.411
Gnomad4 ASJ
AF:
0.600
Gnomad4 EAS
AF:
0.209
Gnomad4 SAS
AF:
0.382
Gnomad4 FIN
AF:
0.384
Gnomad4 NFE
AF:
0.451
Gnomad4 OTH
AF:
0.411
Alfa
AF:
0.403
Hom.:
5499
Bravo
AF:
0.376
Asia WGS
AF:
0.292
AC:
1015
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.59
DANN
Benign
0.93

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: rs10508717; hg19: chr10-26672328; API