chr10-129466472-G-A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The ENST00000735692.1(ENSG00000296036):​n.95+1094C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00739 in 152,206 control chromosomes in the GnomAD database, including 4 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 0.0074 ( 4 hom., cov: 32)

Consequence

ENSG00000296036
ENST00000735692.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.72

Publications

3 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 -8 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BS2
High Homozygotes in GnomAd4 at 4 gene

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
ENSG00000296036ENST00000735692.1 linkn.95+1094C>T intron_variant Intron 1 of 3

Frequencies

GnomAD3 genomes
AF:
0.00740
AC:
1125
AN:
152088
Hom.:
4
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00273
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00982
Gnomad ASJ
AF:
0.00663
Gnomad EAS
AF:
0.000580
Gnomad SAS
AF:
0.00767
Gnomad FIN
AF:
0.00330
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.0109
Gnomad OTH
AF:
0.0110
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00739
AC:
1125
AN:
152206
Hom.:
4
Cov.:
32
AF XY:
0.00714
AC XY:
531
AN XY:
74400
show subpopulations
African (AFR)
AF:
0.00272
AC:
113
AN:
41550
American (AMR)
AF:
0.00981
AC:
150
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
0.00663
AC:
23
AN:
3468
East Asian (EAS)
AF:
0.000582
AC:
3
AN:
5156
South Asian (SAS)
AF:
0.00768
AC:
37
AN:
4818
European-Finnish (FIN)
AF:
0.00330
AC:
35
AN:
10596
Middle Eastern (MID)
AF:
0.00680
AC:
2
AN:
294
European-Non Finnish (NFE)
AF:
0.0109
AC:
739
AN:
68000
Other (OTH)
AF:
0.0109
AC:
23
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
58
117
175
234
292
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
20
40
60
80
100
<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:
0.00326
Hom.:
0
Bravo
AF:
0.00796
Asia WGS
AF:
0.00231
AC:
8
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
6.6
DANN
Benign
0.60
PhyloP100
1.7

Splicing

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

Publications

Other links and lift over

dbSNP: rs61859810; hg19: chr10-131264736; API