rs7735506

Variant summary

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

The ENST00000521805.1(ENSG00000253331):​n.496-35596A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.926 in 152,122 control chromosomes in the GnomAD database, including 65,257 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 0.93 ( 65257 hom., cov: 31)

Consequence

ENSG00000253331
ENST00000521805.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.385

Publications

4 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=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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
ENSG00000253331ENST00000521805.1 linkn.496-35596A>T intron_variant Intron 4 of 4 3

Frequencies

GnomAD3 genomes
AF:
0.926
AC:
140761
AN:
152004
Hom.:
65210
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.914
Gnomad AMI
AF:
0.900
Gnomad AMR
AF:
0.962
Gnomad ASJ
AF:
0.928
Gnomad EAS
AF:
0.998
Gnomad SAS
AF:
0.937
Gnomad FIN
AF:
0.942
Gnomad MID
AF:
0.946
Gnomad NFE
AF:
0.917
Gnomad OTH
AF:
0.930
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.926
AC:
140865
AN:
152122
Hom.:
65257
Cov.:
31
AF XY:
0.928
AC XY:
69010
AN XY:
74366
show subpopulations
African (AFR)
AF:
0.913
AC:
37922
AN:
41518
American (AMR)
AF:
0.963
AC:
14695
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
0.928
AC:
3223
AN:
3472
East Asian (EAS)
AF:
0.998
AC:
5158
AN:
5168
South Asian (SAS)
AF:
0.937
AC:
4523
AN:
4826
European-Finnish (FIN)
AF:
0.942
AC:
9993
AN:
10608
Middle Eastern (MID)
AF:
0.949
AC:
279
AN:
294
European-Non Finnish (NFE)
AF:
0.917
AC:
62285
AN:
67946
Other (OTH)
AF:
0.931
AC:
1966
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
540
1079
1619
2158
2698
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
906
1812
2718
3624
4530
<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:
0.922
Hom.:
8044
Bravo
AF:
0.928
Asia WGS
AF:
0.958
AC:
3321
AN:
3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.6
DANN
Benign
0.37
PhyloP100
0.39

Splicing

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

Publications

Other links and lift over

dbSNP: rs7735506; hg19: chr5-163581878; API