GeneBe

XR_948500.3:n.198+37664A>G

Variant names:

Variant summary

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

The XR_948500.3(LOC105379048):​n.198+37664A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 152,136 control chromosomes in the GnomAD database, including 30,577 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 0.63 ( 30577 hom., cov: 33)

Consequence

LOC105379048
XR_948500.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.01

Publications

2 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=-0.8).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105379048XR_948500.3 linkn.198+37664A>G intron_variant Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.633
AC:
96295
AN:
152018
Hom.:
30561
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.695
Gnomad AMI
AF:
0.731
Gnomad AMR
AF:
0.636
Gnomad ASJ
AF:
0.705
Gnomad EAS
AF:
0.566
Gnomad SAS
AF:
0.560
Gnomad FIN
AF:
0.594
Gnomad MID
AF:
0.709
Gnomad NFE
AF:
0.606
Gnomad OTH
AF:
0.644
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.633
AC:
96363
AN:
152136
Hom.:
30577
Cov.:
33
AF XY:
0.632
AC XY:
46984
AN XY:
74380
show subpopulations
African (AFR)
AF:
0.695
AC:
28826
AN:
41486
American (AMR)
AF:
0.636
AC:
9720
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.705
AC:
2445
AN:
3470
East Asian (EAS)
AF:
0.565
AC:
2927
AN:
5176
South Asian (SAS)
AF:
0.560
AC:
2701
AN:
4824
European-Finnish (FIN)
AF:
0.594
AC:
6284
AN:
10574
Middle Eastern (MID)
AF:
0.690
AC:
203
AN:
294
European-Non Finnish (NFE)
AF:
0.606
AC:
41231
AN:
68002
Other (OTH)
AF:
0.643
AC:
1359
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1839
3678
5516
7355
9194
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
784
1568
2352
3136
3920
<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:
0.628
Hom.:
4706
Bravo
AF:
0.642
Asia WGS
AF:
0.604
AC:
2101
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
14
DANN
Benign
0.83
PhyloP100
1.0

Splicing

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

Publications

Other links and lift over

dbSNP: rs6867021; hg19: chr5-79229646; API