rs7798431

Variant summary

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

The ENST00000812174.1(ENSG00000286725):​n.297+27734C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,050 control chromosomes in the GnomAD database, including 4,855 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 0.25 ( 4855 hom., cov: 32)

Consequence

ENSG00000286725
ENST00000812174.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.02

Publications

13 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=-0.69).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.459 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
ENSG00000286725ENST00000812174.1 linkn.297+27734C>T intron_variant Intron 2 of 4
ENSG00000286725ENST00000812175.1 linkn.280+27734C>T intron_variant Intron 2 of 5
ENSG00000286725ENST00000812176.1 linkn.297+27734C>T intron_variant Intron 2 of 4

Frequencies

GnomAD3 genomes
AF:
0.245
AC:
37269
AN:
151932
Hom.:
4853
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.195
Gnomad AMI
AF:
0.157
Gnomad AMR
AF:
0.214
Gnomad ASJ
AF:
0.216
Gnomad EAS
AF:
0.441
Gnomad SAS
AF:
0.473
Gnomad FIN
AF:
0.292
Gnomad MID
AF:
0.304
Gnomad NFE
AF:
0.247
Gnomad OTH
AF:
0.254
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.245
AC:
37305
AN:
152050
Hom.:
4855
Cov.:
32
AF XY:
0.253
AC XY:
18788
AN XY:
74346
show subpopulations
African (AFR)
AF:
0.195
AC:
8103
AN:
41472
American (AMR)
AF:
0.215
AC:
3279
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
0.216
AC:
750
AN:
3470
East Asian (EAS)
AF:
0.441
AC:
2282
AN:
5174
South Asian (SAS)
AF:
0.475
AC:
2289
AN:
4816
European-Finnish (FIN)
AF:
0.292
AC:
3081
AN:
10566
Middle Eastern (MID)
AF:
0.299
AC:
88
AN:
294
European-Non Finnish (NFE)
AF:
0.247
AC:
16759
AN:
67962
Other (OTH)
AF:
0.252
AC:
531
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1414
2829
4243
5658
7072
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
412
824
1236
1648
2060
<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:
0.228
Hom.:
2731
Bravo
AF:
0.233
Asia WGS
AF:
0.415
AC:
1438
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
CADD
Benign
6.1
DANN
Benign
0.74
PhyloP100
1.0

Splicing

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

Publications

Other links and lift over

dbSNP: rs7798431; hg19: chr7-25860812; API