rs10879987

Variant summary

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

The ENST00000552856.1(ENSG00000258077):​n.296-40909C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,698 control chromosomes in the GnomAD database, including 9,530 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 0.34 ( 9530 hom., cov: 31)

Consequence

ENSG00000258077
ENST00000552856.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.128

Publications

2 publications found
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105369844XR_007063374.1 linkn.236+16094C>T intron_variant Intron 1 of 6
LOC105369844XR_007063375.1 linkn.236+16094C>T intron_variant Intron 1 of 15
LOC105369844XR_007063376.1 linkn.236+16094C>T intron_variant Intron 1 of 7
LOC105369844XR_007063377.1 linkn.236+16094C>T intron_variant Intron 1 of 7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000258077ENST00000552856.1 linkn.296-40909C>T intron_variant Intron 1 of 4 3
ENSG00000258077ENST00000741358.1 linkn.83+7284C>T intron_variant Intron 1 of 6
ENSG00000258077ENST00000741359.1 linkn.83+7284C>T intron_variant Intron 1 of 6

Frequencies

GnomAD3 genomes
AF:
0.337
AC:
51030
AN:
151578
Hom.:
9542
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.177
Gnomad AMI
AF:
0.382
Gnomad AMR
AF:
0.324
Gnomad ASJ
AF:
0.382
Gnomad EAS
AF:
0.315
Gnomad SAS
AF:
0.316
Gnomad FIN
AF:
0.476
Gnomad MID
AF:
0.459
Gnomad NFE
AF:
0.414
Gnomad OTH
AF:
0.360
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.336
AC:
50991
AN:
151698
Hom.:
9530
Cov.:
31
AF XY:
0.338
AC XY:
25024
AN XY:
74120
show subpopulations
African (AFR)
AF:
0.176
AC:
7295
AN:
41376
American (AMR)
AF:
0.324
AC:
4939
AN:
15248
Ashkenazi Jewish (ASJ)
AF:
0.382
AC:
1322
AN:
3460
East Asian (EAS)
AF:
0.314
AC:
1621
AN:
5164
South Asian (SAS)
AF:
0.315
AC:
1510
AN:
4796
European-Finnish (FIN)
AF:
0.476
AC:
4996
AN:
10496
Middle Eastern (MID)
AF:
0.438
AC:
128
AN:
292
European-Non Finnish (NFE)
AF:
0.414
AC:
28085
AN:
67848
Other (OTH)
AF:
0.355
AC:
748
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1618
3236
4855
6473
8091
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
502
1004
1506
2008
2510
<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:
0.364
Hom.:
1475
Bravo
AF:
0.318
Asia WGS
AF:
0.297
AC:
1036
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.4
DANN
Benign
0.70
PhyloP100
0.13

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs10879987; hg19: chr12-76212219; API