rs17242130

Variant summary

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

The ENST00000781317.1(ENSG00000287938):​n.297+21536A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0795 in 151,512 control chromosomes in the GnomAD database, including 559 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 0.079 ( 559 hom., cov: 31)

Consequence

ENSG00000287938
ENST00000781317.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.648

Publications

3 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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC124901018XR_007058843.1 linkn.230+5057A>C intron_variant Intron 2 of 5
LOC124901018XR_007058844.1 linkn.230+5057A>C intron_variant Intron 2 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000287938ENST00000781317.1 linkn.297+21536A>C intron_variant Intron 3 of 3
ENSG00000287938ENST00000781318.1 linkn.271+21536A>C intron_variant Intron 2 of 2
ENSG00000287938ENST00000781319.1 linkn.152+5830A>C intron_variant Intron 1 of 4

Frequencies

GnomAD3 genomes
AF:
0.0795
AC:
12036
AN:
151410
Hom.:
560
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0507
Gnomad AMI
AF:
0.0538
Gnomad AMR
AF:
0.0731
Gnomad ASJ
AF:
0.0842
Gnomad EAS
AF:
0.000775
Gnomad SAS
AF:
0.0462
Gnomad FIN
AF:
0.0694
Gnomad MID
AF:
0.0918
Gnomad NFE
AF:
0.108
Gnomad OTH
AF:
0.0887
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0795
AC:
12042
AN:
151512
Hom.:
559
Cov.:
31
AF XY:
0.0765
AC XY:
5658
AN XY:
73988
show subpopulations
African (AFR)
AF:
0.0506
AC:
2087
AN:
41272
American (AMR)
AF:
0.0730
AC:
1110
AN:
15210
Ashkenazi Jewish (ASJ)
AF:
0.0842
AC:
292
AN:
3466
East Asian (EAS)
AF:
0.000776
AC:
4
AN:
5152
South Asian (SAS)
AF:
0.0464
AC:
222
AN:
4780
European-Finnish (FIN)
AF:
0.0694
AC:
722
AN:
10408
Middle Eastern (MID)
AF:
0.0952
AC:
28
AN:
294
European-Non Finnish (NFE)
AF:
0.108
AC:
7342
AN:
67914
Other (OTH)
AF:
0.0883
AC:
186
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.510
Heterozygous variant carriers
0
533
1066
1600
2133
2666
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
140
280
420
560
700
<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:
0.0961
Hom.:
1575
Bravo
AF:
0.0795
Asia WGS
AF:
0.0250
AC:
88
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
4.0
DANN
Benign
0.68
PhyloP100
0.65

Splicing

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

Publications

Other links and lift over

dbSNP: rs17242130; hg19: chr5-81154906; API