rs2839632

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000728699.1(ENSG00000295227):​n.114-4225G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.00065 ( 1 hom., cov: 20)
Failed GnomAD Quality Control

Consequence

ENSG00000295227
ENST00000728699.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.132

Publications

3 publications found
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).

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
ENSG00000295227ENST00000728699.1 linkn.114-4225G>A intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.000648
AC:
82
AN:
126576
Hom.:
1
Cov.:
20
show subpopulations
Gnomad AFR
AF:
0.00257
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000173
Gnomad ASJ
AF:
0.000321
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000234
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000814
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000648
AC:
82
AN:
126630
Hom.:
1
Cov.:
20
AF XY:
0.000711
AC XY:
44
AN XY:
61874
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00256
AC:
73
AN:
28532
American (AMR)
AF:
0.000173
AC:
2
AN:
11562
Ashkenazi Jewish (ASJ)
AF:
0.000321
AC:
1
AN:
3114
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5178
South Asian (SAS)
AF:
0.000234
AC:
1
AN:
4276
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
9746
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
234
European-Non Finnish (NFE)
AF:
0.0000814
AC:
5
AN:
61430
Other (OTH)
AF:
0.00
AC:
0
AN:
1696
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.273
Heterozygous variant carriers
0
8
16
25
33
41
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<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:
0.128
Hom.:
454
Asia WGS
AF:
0.156
AC:
548
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.92
DANN
Benign
0.76
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: rs2839632; hg19: chr21-44508207; API