rs1121704

Variant summary

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

The ENST00000555776.1(ENSG00000259097):​n.122-5304C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 151,976 control chromosomes in the GnomAD database, including 9,226 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 0.34 ( 9226 hom., cov: 32)

Consequence

ENSG00000259097
ENST00000555776.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.317

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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105370655XR_001750876.2 linkn.96-5304C>T intron_variant Intron 1 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000259097ENST00000555776.1 linkn.122-5304C>T intron_variant Intron 1 of 2 4
ENSG00000259097ENST00000663808.2 linkn.206-5304C>T intron_variant Intron 2 of 3

Frequencies

GnomAD3 genomes
AF:
0.342
AC:
51990
AN:
151858
Hom.:
9226
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.304
Gnomad AMI
AF:
0.355
Gnomad AMR
AF:
0.297
Gnomad ASJ
AF:
0.368
Gnomad EAS
AF:
0.0927
Gnomad SAS
AF:
0.309
Gnomad FIN
AF:
0.366
Gnomad MID
AF:
0.396
Gnomad NFE
AF:
0.391
Gnomad OTH
AF:
0.353
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.342
AC:
52012
AN:
151976
Hom.:
9226
Cov.:
32
AF XY:
0.338
AC XY:
25093
AN XY:
74264
show subpopulations
African (AFR)
AF:
0.304
AC:
12613
AN:
41468
American (AMR)
AF:
0.296
AC:
4523
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.368
AC:
1275
AN:
3466
East Asian (EAS)
AF:
0.0927
AC:
479
AN:
5168
South Asian (SAS)
AF:
0.308
AC:
1478
AN:
4806
European-Finnish (FIN)
AF:
0.366
AC:
3863
AN:
10552
Middle Eastern (MID)
AF:
0.391
AC:
115
AN:
294
European-Non Finnish (NFE)
AF:
0.391
AC:
26596
AN:
67944
Other (OTH)
AF:
0.356
AC:
749
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1735
3470
5206
6941
8676
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
520
1040
1560
2080
2600
<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:
0.354
Hom.:
1214
Bravo
AF:
0.335
Asia WGS
AF:
0.223
AC:
777
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.4
DANN
Benign
0.50
PhyloP100
-0.32

Splicing

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

Publications

Other links and lift over

dbSNP: rs1121704; hg19: chr14-98552166; API