rs7277820

Variant summary

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

The ENST00000787142.1(ENSG00000302472):​n.208-8383T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,188 control chromosomes in the GnomAD database, including 23,011 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 0.54 ( 23011 hom., cov: 33)

Consequence

ENSG00000302472
ENST00000787142.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.688

Publications

12 publications found
Variant links:
Genes affected
DSCR9 (HGNC:16301): (Down syndrome critical region 9)

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=-0.81).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 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
ENSG00000302472ENST00000787142.1 linkn.208-8383T>C intron_variant Intron 1 of 2
ENSG00000302472ENST00000787143.1 linkn.185+9985T>C intron_variant Intron 1 of 1
ENSG00000302472ENST00000787144.1 linkn.212-7381T>C intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.543
AC:
82520
AN:
152070
Hom.:
22979
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.646
Gnomad AMI
AF:
0.356
Gnomad AMR
AF:
0.583
Gnomad ASJ
AF:
0.405
Gnomad EAS
AF:
0.602
Gnomad SAS
AF:
0.591
Gnomad FIN
AF:
0.562
Gnomad MID
AF:
0.513
Gnomad NFE
AF:
0.469
Gnomad OTH
AF:
0.548
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.543
AC:
82601
AN:
152188
Hom.:
23011
Cov.:
33
AF XY:
0.546
AC XY:
40642
AN XY:
74388
show subpopulations
African (AFR)
AF:
0.645
AC:
26801
AN:
41534
American (AMR)
AF:
0.583
AC:
8916
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
0.405
AC:
1405
AN:
3468
East Asian (EAS)
AF:
0.602
AC:
3111
AN:
5166
South Asian (SAS)
AF:
0.592
AC:
2857
AN:
4830
European-Finnish (FIN)
AF:
0.562
AC:
5953
AN:
10598
Middle Eastern (MID)
AF:
0.510
AC:
150
AN:
294
European-Non Finnish (NFE)
AF:
0.470
AC:
31919
AN:
67982
Other (OTH)
AF:
0.553
AC:
1166
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1957
3914
5872
7829
9786
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
712
1424
2136
2848
3560
<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:
0.490
Hom.:
10832
Bravo
AF:
0.544
Asia WGS
AF:
0.613
AC:
2135
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
13
DANN
Benign
0.81
PhyloP100
0.69

Splicing

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

Publications

Other links and lift over

dbSNP: rs7277820; hg19: chr21-38580309; API