GeneBe

rs4769989

Variant names:

Variant summary

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

The XR_941720.2(LOC105370102):​n.106+4978A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 152,006 control chromosomes in the GnomAD database, including 22,848 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 0.54 ( 22848 hom., cov: 32)

Consequence

LOC105370102
XR_941720.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.455

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=-0.84).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105370102XR_941720.2 linkn.106+4978A>G intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.545
AC:
82741
AN:
151888
Hom.:
22824
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.545
Gnomad AMI
AF:
0.626
Gnomad AMR
AF:
0.531
Gnomad ASJ
AF:
0.516
Gnomad EAS
AF:
0.237
Gnomad SAS
AF:
0.507
Gnomad FIN
AF:
0.529
Gnomad MID
AF:
0.481
Gnomad NFE
AF:
0.577
Gnomad OTH
AF:
0.536
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.545
AC:
82812
AN:
152006
Hom.:
22848
Cov.:
32
AF XY:
0.539
AC XY:
40051
AN XY:
74300
show subpopulations
African (AFR)
AF:
0.545
AC:
22584
AN:
41426
American (AMR)
AF:
0.531
AC:
8118
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.516
AC:
1792
AN:
3470
East Asian (EAS)
AF:
0.237
AC:
1224
AN:
5174
South Asian (SAS)
AF:
0.508
AC:
2446
AN:
4816
European-Finnish (FIN)
AF:
0.529
AC:
5583
AN:
10558
Middle Eastern (MID)
AF:
0.493
AC:
145
AN:
294
European-Non Finnish (NFE)
AF:
0.577
AC:
39216
AN:
67966
Other (OTH)
AF:
0.538
AC:
1133
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1915
3829
5744
7658
9573
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
718
1436
2154
2872
3590
<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:
0.564
Hom.:
77495
Bravo
AF:
0.545
Asia WGS
AF:
0.445
AC:
1548
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.98
DANN
Benign
0.81
PhyloP100
-0.46

Splicing

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

Publications

Other links and lift over

dbSNP: rs4769989; hg19: chr13-20874910; API