chr17-17402773-A-G

Variant summary

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

The ENST00000770697.1(ENSG00000300301):​n.405+3566T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,156 control chromosomes in the GnomAD database, including 1,888 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 0.15 ( 1888 hom., cov: 32)

Consequence

ENSG00000300301
ENST00000770697.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.57

Publications

5 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=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 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
ENSG00000300301ENST00000770697.1 linkn.405+3566T>C intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.151
AC:
22885
AN:
152038
Hom.:
1875
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.226
Gnomad AMI
AF:
0.106
Gnomad AMR
AF:
0.128
Gnomad ASJ
AF:
0.168
Gnomad EAS
AF:
0.116
Gnomad SAS
AF:
0.152
Gnomad FIN
AF:
0.0889
Gnomad MID
AF:
0.142
Gnomad NFE
AF:
0.122
Gnomad OTH
AF:
0.147
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.151
AC:
22934
AN:
152156
Hom.:
1888
Cov.:
32
AF XY:
0.148
AC XY:
11018
AN XY:
74400
show subpopulations
African (AFR)
AF:
0.226
AC:
9395
AN:
41496
American (AMR)
AF:
0.128
AC:
1959
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.168
AC:
583
AN:
3468
East Asian (EAS)
AF:
0.116
AC:
603
AN:
5184
South Asian (SAS)
AF:
0.152
AC:
731
AN:
4820
European-Finnish (FIN)
AF:
0.0889
AC:
943
AN:
10606
Middle Eastern (MID)
AF:
0.146
AC:
43
AN:
294
European-Non Finnish (NFE)
AF:
0.122
AC:
8273
AN:
67984
Other (OTH)
AF:
0.145
AC:
307
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
964
1929
2893
3858
4822
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
258
516
774
1032
1290
<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:
0.134
Hom.:
1396
Bravo
AF:
0.157
Asia WGS
AF:
0.150
AC:
523
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.62
DANN
Benign
0.33
PhyloP100
-1.6

Splicing

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

Publications

Other links and lift over

dbSNP: rs1569040; hg19: chr17-17306087; API