rs17041907

Variant summary

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

The ENST00000691919.3(ENSG00000287042):​n.259-9270A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.061 in 152,086 control chromosomes in the GnomAD database, including 379 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 0.061 ( 379 hom., cov: 31)

Consequence

ENSG00000287042
ENST00000691919.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.345
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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC124906217XR_007095836.1 linkn.86-152T>G intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000287042ENST00000691919.3 linkn.259-9270A>C intron_variant Intron 3 of 3
ENSG00000287042ENST00000702385.2 linkn.293-9270A>C intron_variant Intron 3 of 3
ENSG00000287042ENST00000702609.2 linkn.217-9270A>C intron_variant Intron 3 of 3

Frequencies

GnomAD3 genomes
AF:
0.0611
AC:
9279
AN:
151968
Hom.:
378
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0785
Gnomad AMI
AF:
0.0164
Gnomad AMR
AF:
0.0400
Gnomad ASJ
AF:
0.0300
Gnomad EAS
AF:
0.209
Gnomad SAS
AF:
0.0771
Gnomad FIN
AF:
0.0627
Gnomad MID
AF:
0.0506
Gnomad NFE
AF:
0.0453
Gnomad OTH
AF:
0.0464
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0610
AC:
9283
AN:
152086
Hom.:
379
Cov.:
31
AF XY:
0.0623
AC XY:
4633
AN XY:
74328
show subpopulations
African (AFR)
AF:
0.0783
AC:
3250
AN:
41484
American (AMR)
AF:
0.0400
AC:
612
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
0.0300
AC:
104
AN:
3466
East Asian (EAS)
AF:
0.208
AC:
1074
AN:
5152
South Asian (SAS)
AF:
0.0771
AC:
370
AN:
4796
European-Finnish (FIN)
AF:
0.0627
AC:
664
AN:
10594
Middle Eastern (MID)
AF:
0.0510
AC:
15
AN:
294
European-Non Finnish (NFE)
AF:
0.0453
AC:
3081
AN:
67994
Other (OTH)
AF:
0.0464
AC:
98
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
437
875
1312
1750
2187
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
112
224
336
448
560
<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:
0.0488
Hom.:
325
Bravo
AF:
0.0608
Asia WGS
AF:
0.113
AC:
394
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
5.6
DANN
Benign
0.71
PhyloP100
0.34

Splicing

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

Publications

Other links and lift over

dbSNP: rs17041907; hg19: chr3-16169628; API