rs17197908

Variant summary

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

The ENST00000744989.1(ENSG00000297050):​n.48+4570G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 151,768 control chromosomes in the GnomAD database, including 3,641 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 0.19 ( 3641 hom., cov: 31)

Consequence

ENSG00000297050
ENST00000744989.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.557

Publications

1 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=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 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
ENSG00000297050ENST00000744989.1 linkn.48+4570G>T intron_variant Intron 1 of 4
ENSG00000297050ENST00000744990.1 linkn.70+4570G>T intron_variant Intron 1 of 5

Frequencies

GnomAD3 genomes
AF:
0.195
AC:
29552
AN:
151650
Hom.:
3642
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0568
Gnomad AMI
AF:
0.306
Gnomad AMR
AF:
0.168
Gnomad ASJ
AF:
0.212
Gnomad EAS
AF:
0.0624
Gnomad SAS
AF:
0.137
Gnomad FIN
AF:
0.334
Gnomad MID
AF:
0.199
Gnomad NFE
AF:
0.275
Gnomad OTH
AF:
0.199
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.195
AC:
29552
AN:
151768
Hom.:
3641
Cov.:
31
AF XY:
0.195
AC XY:
14470
AN XY:
74128
show subpopulations
African (AFR)
AF:
0.0566
AC:
2348
AN:
41468
American (AMR)
AF:
0.167
AC:
2541
AN:
15194
Ashkenazi Jewish (ASJ)
AF:
0.212
AC:
736
AN:
3468
East Asian (EAS)
AF:
0.0627
AC:
323
AN:
5148
South Asian (SAS)
AF:
0.136
AC:
655
AN:
4802
European-Finnish (FIN)
AF:
0.334
AC:
3516
AN:
10532
Middle Eastern (MID)
AF:
0.201
AC:
59
AN:
294
European-Non Finnish (NFE)
AF:
0.275
AC:
18672
AN:
67842
Other (OTH)
AF:
0.201
AC:
423
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1148
2295
3443
4590
5738
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
322
644
966
1288
1610
<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:
0.240
Hom.:
994
Bravo
AF:
0.177
Asia WGS
AF:
0.141
AC:
492
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.51
DANN
Benign
0.66
PhyloP100
-0.56

Splicing

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

Publications

Other links and lift over

dbSNP: rs17197908; hg19: chr13-38175744; API